Accurate structure prediction of biomolecular interactions with AlphaFold 3

2024/05/08 by Josh Abramson, Jonas Adler, Jack Dunger +45 · 1 voice · 958 citations
Biochemistry, Genetics and Molecular Biology · #Protein Structure and Dynamics

paper · pdf · doi:10.1038/s41586-024-07487-w

openalex publication_date 2024/05/08 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31

Abstract

Abstract The introduction of AlphaFold 2 1 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design 2–6 . Here we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture that is capable of predicting the joint structure of complexes including proteins, nucleic acids, small molecules, ions and modified residues. The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for protein–ligand interactions compared with state-of-the-art docking tools, much higher accuracy for protein–nucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibody–antigen prediction accuracy compared with AlphaFold-Multimer v.2.3 7,8 . Together, these results show that high-accuracy modelling across biomolecular space is possible within a single unified deep-learning framework.

Citations

• AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
• Highly accurate protein structure prediction with AlphaFold
• Accurate prediction of protein structures and interactions using a three-track neural network
• State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
• DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
• Survey of Hallucination in Natural Language Generation
• Evolutionary-scale prediction of atomic-level protein structure with a language model
• Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom
• Scoring function for automated assessment of protein structure template quality

Cited by

• InstructPro: Natural Language Guided Ligand-Binding Protein Design
• SUN5 forms a regular protein lattice reinforcing the sperm head–tail junction
• Multiple Roles of Protamine Kinase SRPK1 and Phosphatase PP1γ in Sperm Development
• Multicyclic D‐Stereospecific Hydrolase Dimer With High Sustained Activity
• A Wnt-induced conformational phospho-switch in DVL3 controls interaction with Frizzled receptors and Wnt/β-catenin signaling
• Embracing Evolution: A Call for Body-Control Co-Design in Embodied Humanoid Robot
• Use of tandem‐affinity chromatography to incorporate nucleotide loading of small GTPases during their purification
• Synergistic engineering of Casδ nuclease for robust genome editing
• Structure-based prediction reveals a difference in the binding mode of anti-BCMA antibodies to BCMA and soluble BCMA
• Architecture of the 8 MDa Hdr–Vhu–Fwd super-assembly in class I methanogens
• Histone diversity in the archaeal domain of life
• Artificial intelligence in bioinformatics: a survey
• CATVariant: a web server for integrated protein variant interpretation across sequence, structure, population, and clinical evidence
• How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution
• Revealing deep evolutionary relationships between RNA viruses using predicted structural models of viral RNA polymerases
• Functional analyses identify the L1 ORF2p Cryptic domain as a hub for intramolecular interfaces required for retrotransposition
• A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions
• Assessing the validity of leucine zipper constructs predicted by AlphaFold
• Ancestral Chaperonins Provide the First Structural Glimpse into Early Multimeric Protein Evolution
• FASTK post-transcriptional regulators – a ‘FAST-tracK’ in mitochondrial gene expression
• Genomic Insights Into Convergent Evolution: Adaptation to Rocky Habitats in Rock-Inhabiting Fungi
• Allosteric regulation of fungal fatty acid synthesis
• Functional and Structural Studies on the Esperamicin Thioesterase and Progress toward Understanding Enediyne Core Biosynthesis
• Nitrate reduction salvage pathway in Methanococcales
• Artificial intelligence-driven design of inorganic materials for biomedical applications
• Transcription factor collaboration enables precise T cell state engineering
• Nucleosome positioning shapes cryptic antisense transcription
• Functional characterization of two O ‑methyltransferases and a glycosyltransferase catalyzing the last two steps of phillyrin biosynthesis in Forsythia suspensa
• Unifying principles for the design and evaluation of natural product-inspired compound collections
• SH3BP5L triggers the RAB11A-regulated integrin recycling network implicated in breast cancer metastasis
• B-PPI: A Cross-Attention Model for Large-Scale Bacterial Protein-Protein Interaction Prediction
• Structural modeling and biochemical characterization of MSMEG₀748, a MoxR ATPase from Mycobacterium smegmatis
• Cryo-EM structure of the QseG-QseE complex reveals an accessory protein-driven two-component system activation mechanism
• Employing deep mutational scanning in the Escherichia coli periplasm to decode the thermodynamic landscape for amyloid formation
• Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned
• Deciphering the evolutionary origin of the enantioselectivity of short-chain dehydrogenases from plants toward 1-borneol
• Review of protein structure-based analyses that illuminate plant stress mechanisms
• Harnessing AlphaFold to reveal hERG channel conformational state secrets
• Sweeps in Space: Leveraging Geographic Data to Identify Beneficial Alleles in Anopheles gambiae
• Targeting protein disorder: the next hurdle in drug discovery
• Structural analysis of the NifL-NifA complex reveals the molecular basis of anti-activation of nitrogen fixation gene expression in Azotobacter vinelandii
• Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea
• The Magnaporthe oryzae effector Pwl2 alters HIPP43 localization to suppress host immunity
• A Pedigree-Based Map of Crossovers and Noncrossovers in Aye-Ayes ( Daubentonia madagascariensis )
• The Spc105/Kre28 complex promotes mitotic error correction by outer kinetochore recruitment of Ipl1/Sli15
• Computational advances in discovering cryptic pockets for drug discovery
• Epitope landscape in autoimmune neurological disease and beyond
• The aptamer BT200 blocks interaction of K1405-K1408 in the VWF-A1 domain with macrophage LRP1
• Sla2 is a core interaction hub for Clathrin Light Chain and the Pan1/End3/Sla1 Complex
• Evolving strategies for virus discovery
• Acyl Carrier Protein is Essential for Apicoplast Biogenesis in Malaria Parasites Independent of Fatty Acid Synthesis
• Red-shifted GRAB acetylcholine sensors for multiplex imaging in vivo
• Evolutionary analysis of transcription elongation factors reveals conserved and lineage-specific regulatory domains
• Isolation and characterization of broad-range Staphylococcus epidermidis sepunaviruses
• AI-guided discovery of atypical protein assemblies
• Manganese homeostasis supports Stenotrophomonas maltophilia oxidative stress defense and replication in Acanthamoeba castellanii phagosomes
• Ribosome collisions trigger tmRNA-mediated rescue through mRNA disengagement
• The barley m6A demethylase HvALKBH1B undergoes phase separation to enhance immunity to a plant rhabdovirus
• Intelectin-2 is a broad-spectrum antimicrobial lectin
• Sorghum embryos undergoing B chromosome elimination express B-variants of mitotic-related genes
• Origin and Evolution of Very Large Extracellular Proteins in Fructophilic Lactic Acid Bacteria
• Molecular determinants underlying NPH3 condensation and function in phototropism: an integrative approach
• Modulation of GSNOR activity for improved NO homeostasis and flood resilience in plants
• Deciphering the biochemical functions and nucleotide sugar donor specificity determinants of dicot GT61 glycosyltransferases involved in xylan substitutions
• AlphaFold3 for Structure-guided Ligand Discovery
• Associations between sickle haemoglobin and the Plasmodium falciparum CLAG and FIKK gene families revealed by meta-analysis of 6,289 African samples
• Evolutionary Refinement of Mitochondrial and Plastid Targeting Sequences Coincides with the Late Diversification of Land Plants
• Generation of protein dynamics by machine learning
• Recent advances in the inference of deep viral evolutionary history
• Silencing lipid catabolism determines longevity in response to fasting
• Analysis of protease production in the microbial antagonist Pythium oligandrum and host/prey Pythium myriotylum protease inhibitors
• Generative AI for synthetic biology: Designing biological parts, circuits, and genomes
• Loss of FBXO11 establishes a stem cell program in acute myeloid leukemia by dysregulating LONP1
• And… cut! – how conformational regulation of CRISPR-Cas effectors directs nuclease activity
• Cyanobacteriochrome-like GAF folds in phages revealed via AlphaFold proteomic modelling
• Learning the language of plant immunity: opportunities and challenges for AI-assisted modelling of fungal effector x host protein complexes
• The characterization of the LEAFY COTYLEDON 2 activation domains reveals its conserved dual mode of action in flowering plants
• The generative era of medical AI
• Evolution of linear triterpenoid biosynthesis within the Euphorbia genus
• Identification of cognate recombination directionality factors for large serine recombinases by virtual pulldown
• Making plant tissue accessible for cryo-electron tomography
• Artificial intelligence-driven computational methods for antibody design and optimization
• Function and firing of the Streptomyces coelicolor contractile injection system requires the membrane protein CisA
• A new heme enzyme family forms hydrazine groups in diverse biosynthetic pathways
• Exploring the function of plant root diffusion barriers in sealing and shielding for environmental adaptation
• Thiotemplated Polyketide Chain Fusion and Reductive Cyclization Build the Reactive Butenolide Core of Malleicyprol
• Environmental reservoir of resistance genes for the last resort antibiotic Cefiderocol
• Assessment of Nucleic Acid Structure Prediction in CASP16
• LINE-1 ribonucleoprotein condensates bind DNA to enable nuclear entry during mitosis
• Barlow Twins deep neural network for advanced 1D drug–target interaction prediction
• Homospermidine synthase evolution and the origin(s) of pyrrolizidine alkaloids in Apocynaceae
• A female-specific RdDM-associated element guides de novo DNA methylation during rice gametophyte development
• Big data and artificial intelligence‐aided crop breeding: Progress and prospects
• A Nuclear Effector of Magnaporthe oryzae Targets a Mitogen-Activated Protein Kinase to Suppress Basal Plant Defense
• Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles
• Evolutionary History and Functional Divergence of Hydroxycarboxylic Acid Receptors in Primates
• AcuB senses cellular energy charge to coordinate acetyl-CoA synthesis in bacteria
• From sequence to scaffold: Computational design of protein nanoparticle vaccines from AlphaFold2-predicted building blocks
• Phase separation of an FtAT-hook transcription factor regulates seed development under heat stress in Tartary buckwheat
• Different modes of engagement with the nucleosome acidic patch yield distinct functional outcomes
• Re-investigation of the HExxH enzyme DarF reveals a dehydrogenation–epoxidation reaction
• Symbiotic peptides modulate rhizobial physiology without terminal differentiation
• IMMREP25: Unseen Peptides
• Emerging technologies for the discovery of biosynthetic genes in plants
• How are evolutionarily young and old proteins distributed in sequence space?
• How is the Amyloid Fold Built? Polymorphism and the Microscopic Mechanisms of Fibril Assembly
• Stability and cooperativity in chimeric de novo TIM barrels via quarter swapping
• Engineering a self‐organized enzyme cascade for enhanced cell‐free biosynthesis of 3‐hydroxypropionic acid
• Analysis of the heterogenous structural states of the hexameric ATPase PilU of the type IV pili from Vibrio cholerae
• Intrinsic conformational equilibria position arrestin‐2 for activation
• AI‐Physics‐Experiment Trinity for Integrated Protein Dynamics Modeling
• Leveraging large language models to predict antibody biological activity against influenza A hemagglutinin
• Mind the gap: the challenges and opportunities for genomics-driven harnessing of plant metabolic diversity for therapeutic applications
• CsmR controls both, motility and cell shape, in Haloferax volcanii
• A conserved aspartate residue in [4Fe-4S]-containing HypD is required for [NiFe]-cofactor biosynthesis and for efficient interaction of the HypCD scaffold complex with HypE
• The Kinesin-14 tail: Dual microtubule binding domains drive spindle morphogenesis through tight microtubule cross-linking and robust sliding
• High-Performance Chemigenetic Potassium Ion Indicator
• Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment
• Machine-guided dual-objective protein engineering for deimmunization and therapeutic functions
• Inhibition of VP2-mediated entry: a potential antiviral strategy to treat or prevent calicivirus disease
• Enhancing RNA 3D Structure Prediction: A Hybrid Approach Combining Expert Knowledge and Computational Tools in CASP16
• AlphaFold3 at CASP16
• Subcellular localization as a driver of protein function
• Innovations in Silicon Transport Shaped the Rise of Biosilicification and Skeletal Evolution in Sponges
• Telomeric transposons are pervasive in linear bacterial genomes
• Complexome profiling of the Chlamydomonas psb28 mutant reveals TEF5 as an early PSII assembly factor
• TTF2 drives mitotic replisome disassembly and MiDAS by coupling the TRAIP ubiquitin ligase to Polε
• ConforNets: Latents-Based Conformational Control in OpenFold3
• Integrating glycosylation in de novo protein design with ReGlyco Binder Design Filter
• Direct evidence of acid-driven protein desolvation
• DefensePredictor: A machine learning model to discover prokaryotic immune systems
• Beyond sequences: structure-guided discovery of novel protein functions in plants
• Identification and structural characterization of anthrax toxin receptor 2 as the Clostridium perfringens NetF receptor
• H 2 ‐dependent modulation of tetrahydromethanopterin S‐methyltransferase (Mtr complex) activity by the small protein MtrR in Methanosarcina mazei
• Predictors of Protein Evolution in the drosophilid Immune System
• A Specific Sinorhizobium Flagellin Suppresses Legume Nodulation Through Immune Activation
• Structure and mechanism of antiphage retron Eco2
• Structural and evolutionary insights into the isoprene monooxygenases
• Contrastive Geometric Learning Unlocks Unified Structure- and Ligand-Based Drug Design
• The ancient E-ring in bacterial flagellar motors
• A Comparative Analysis of Receptor‐Like Kinases in Chlorophyta Reveals the Presence of Putative Cell Wall Integrity Sensors
• A recurrent adaptive mutation in the transmembrane 2B protein of an insect picorna-like virus in a nonnative host
• Pearl: A Foundation Model for Placing Every Atom in the Right Location
• Synergizing chemical and AI communities for advancing laboratories of the future
• Machine learning approaches for interpretable antibody property prediction using structural data
• A rapid and high-throughput biotechnology quantifies major glycoforms of human IgG1 mAb drugs
• Connecting the dots: deep learning-based automated model building methods in cryo-EM
• Studying the long-term adaptation of Haloferax volcanii to low salt conditions: transcriptomic and genetic analyses
• Unlocking the benefits of transparent and reusable science for climate risk management
• Engineering antigenic breadth against SARS-CoV-2 by pairing divergent RBDs within a single mRNA immunogen
• PexR is a noncanonical regulator of the peroxide stress response in bacteria
• Genomic investigations in animal enteric disease-associated Clostridium perfringens
• All the world’s a phage
• Noncatalytic functions of ISOAMYLASE 1 and 2 affect the proportion of insoluble and soluble α-polyglucans in maize
• Uncovering Convergent Pattern Recognition Receptors Recognising Phytophthora Across Plant Lineages
• A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome
• Structural basis of the catalytic and allosteric mechanism of bacterial acetyltransferase PatZ
• BioPipelines: Accessible Computational Protein and Ligand Design for Chemical Biologists
• Pseudogenization of the chaperonin system in ‘Candidatus Phytoplasma pruni’ revealed by genome sequencing and comparative genomics
• A simple cell-cycle control system in Marchantia polymorpha provides a framework for understanding plant cell proliferation
• Identification of a highly expressed gene cluster likely coding for benzene activation enzymes in a methanogenic enrichment culture
• Engineering Herbicide Cross‐Resistance in Rapeseed by Generating Stacked BnaALS Mutations via Sequential CBE and ABE8e ‐ SpRY Editing
• Opportunities for artificial intelligence and synthetic biology in designing living drug delivery systems
• How the non-motile kinesin KIF7 adapts conserved kinesin principles for its function in Hedgehog signaling
• Functional analysis of a diterpene synthase for jiangxidienes and jiangxienols biosynthesis from Streptacidiphilus jiangxiensis
• Calmodulin-dependent protein kinase-related kinase CRK5 contributes to the regulation of the PIN3 cellular localization domain upon plant weight increase
• ExplainBind: Explainable Physicochemical Determinants of Protein–Ligand Binding via Non-Covalent Interactions
• Ungrounding intelligence: From biological minds to artificial cognition
• Unraveling the Link Between Thermal Adaptation and Latent Allostery in Malate Dehydrogenase From Methanococcales
• Class A PBPs reinforce the septal cell wall following initial synthesis by SEDS–bPBP pairs during bacterial cytokinesis
• Navigating protein–nucleic acid sequence-structure landscapes with deep learning
• CryoDyna: Multiscale end-to-end modeling of cryo-EM macromolecule dynamics with physics-aware neural network
• Plant mobile domain protein–DNA motif modules counteract Polycomb silencing to stabilize gene expression
• A nanoluciferase-tagged Schmallenberg virus (SBV): an efficient tool for measuring and tracking viral infection dynamics
• AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?
• Modeling flexible RNA 3D structures and RNA-protein complexes
• The Type VI Secretion System of Sinorhizobium fredii USDA257 Is Required for Successful Nodulation With Glycine max cv Pekin
• The histone chaperone Spt6 controls chromatin structure through its conserved N-terminal domain
• RNA-induced PRC2 inhibition depends on the sequence of bound RNA
• FOXQ1 Regulates Brain Endothelial Mitochondrial Function by Orchestrating Calcium Signaling and Cristae Morphology
• Structure of Pex8 in complex with peroxisomal receptor Pex5 reveals its essential role in peroxisomal cargo translocation
• Relaxed Sequence Sampling for Diverse Protein Design
• Regulation of a phage defence island by RptR, a novel repressor that controls restriction–modification systems in diverse bacteria
• Harnessing Small RNAs as Synthetic Post-transcriptional Regulators in Bacteria
• AI-based antibody design targeting recent H5N1 avian influenza strains
• Solanum bulbocastanum nucleotide‐binding leucine‐rich repeat receptor evolution reveals functional variants and critical residues in Rpi‐blb1/RB
• Structural Enzymology, Phylogenetics, Differentiation, and Symbolic Reflexivity at the Dawn of Biology
• Beyond venomous fangs: Uloboridae spiders have lost their venom but not their toxicity
• Evolutionary Insights into the Length Variation of DNA Damage Response Proteins Across Eukaryotes
• Protein Folding with Neural Ordinary Differential Equations
• ODesign: A World Model for Biomolecular Interaction Design
• RiboPO: Preference Optimization for Structure- and Stability-Aware RNA Design
• On Uncertainty Calibration for Equivariant Functions
• Structural and functional implications of phase separation of membrane protein LacY in Escherichia coli
• Insights into the Unknown: Federated Data Diversity Analysis on Molecular Data
• Protein generation with embedding learning for motif diversification
• Human languages trade off complexity against efficiency
• Warm temperature–induced autophagy mediates selective degradation of TIMING OF CAB EXPRESSION 1 thus promoting plant thermomorphogenesis
• Triangle Multiplication Is All You Need For Biomolecular Structure Representations
• Target Engagement Assays in Early Drug Discovery
• p53-inducible lncRNA LOC644656 causes genotoxic stress-induced stem cell maldifferentiation and cancer chemoresistance
• FcRn-silencing of IL-12Fc prevents toxicity of local IL-12 therapy and prolongs survival in experimental glioblastoma
• Biosynthesis and assembly of hydrogenase [NiFe]-cofactor: recent advances and perspectives
• Integrating Intermediate Traits in Phylogenetic Genotype-to-Phenotype Studies
• Cotton Plants Presenting Symptoms Associated with Cotton Leafroll Dwarf Virus Revealed a Novel Caulimovirid, Cotton Virus A, with Endogenous Caulimovirids in Its Hosts
• Cross-disciplinary perspectives on the potential for artificial intelligence across chemistry
• TOM20-driven E3 ligase recruitment regulates mitochondrial dynamics through PLD6
• Metagenomic mining reveals novel viral histones in dsDNA viruses
• ZYG-12/Hook's dual role as a dynein adaptor for early endosomes and nuclei is regulated by alternative splicing of its cargo binding domain
• Machine learning to dissect perturbations in complex cellular systems
• AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins
• Atomically accurate de novo design of antibodies with RFdiffusion
• Target of Rapamycin (TOR): A Master Regulator in Plant Growth, Development, and Stress Responses
• Are protein language models the new universal key?
• Simulating 500 million years of evolution with a language model
• Pedoman Peri-operatif Renal Assessment
• Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure
• Protein Language Models: Is Scaling Necessary?
• Evaluating protein binding interfaces with PUMBA
• Capturing Protein Free Energy Landscape using Efficient Quantum Encoding
• 3D-GSRD: 3D Molecular Graph Auto-Encoder with Selective Re-mask Decoding
• FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction
• AB-UPT for Automotive and Aerospace Applications
• Matcha: Multi-Stage Riemannian Flow Matching for Accurate and Physically Valid Molecular Docking
• Counting Hallucinations in Diffusion Models
• SimPoly: Simulation of Polymers with Machine Learning Force Fields Derived from First Principles
• Precision Design of Cyclic Peptides using AlphaFold
• Catalytic p K a Attenuation in a Hydrolytic Metalloenzyme by Genetic Code Expansion
• Artificial Intelligence Virtual Cells: From Measurements to Decisions across Modality, Scale, Dynamics, and Evaluation
• Functional Screen of Wilson Disease ATP7B Variants Reveals Residual Transport Activities
• Structural Insights Into Thyroid Hormone Receptors
• PAINT: Parallel-in-time Neural Twins for Dynamical System Reconstruction
• Reproducibility: The New Frontier in AI Governance
• Generative AI for Biosciences: Emerging Threats and Roadmap to Biosecurity
• Protenix-Mini+: efficient structure prediction model with scalable pairformer
• Latent Retrieval Augmented Generation of Cross-Domain Protein Binders
• ProteinAE: Protein Diffusion Autoencoders for Structure Encoding
• Structure Bioinformatics of Six Human Integral Transmembrane Enzymes and their AlphaFold3 Predicted Water-Soluble QTY Analogs: Insights into FACE1 and STEA4 Binding Mechanisms
• Generative design of synthetic gene circuits for functional and evolutionary properties
• Structural insights into HRI kinase activity and inhibition
• Predicting Biomolecular Interactions in the Next Decade:Physics-Based Methods Meet AI-Driven Approaches
• Evolutionary History of the α-Carbonic Anhydrase Gene Family in the Phylum Arthropoda, With Comparisons to αCA in Chordates
• Mechanisms controlling the plasma membrane targeting and the nanodomain organization of the plant SPFH protein HIR2
• Chemically tunable permeability of engineered alpha-Hemolysin in synthetic cells
• Higher-order assembly of a type IX retron enables exploitation for designer antimicrobials
• A Chromatin Biology Assessment of AlphaFold3
• A conserved structural logic underlies sensor–helper NLR communication in the NRC immune receptor network
• Shaping the future of probiotics, live biotherapeutic products, and fecal microbiota transplantation: 30 scientific recommendations from the CHINAGUT Conference
• An Alternative Trajectory for Generative AI
• Autonomous Agents for Scientific Discovery: Orchestrating Scientists, Language, Code, and Physics
• Matching the Optimal Denoiser in Point Cloud Diffusion with (Improved) Rotational Alignment
• Scaling Laws and Symmetry, Evidence from Neural Force Fields
• Maple: A Multi-agent System for Portable Deep Learning across Clusters
• Physically Valid Biomolecular Interaction Modeling with Gauss-Seidel Projection
• Identification of intracellular target of antimicrobial peptide EWAMP-R in bacteria
• Inducing TRIB2-targeted protein degradation to reverse chemoresistance in acute myeloid leukaemia
• Several plant self‐incompatibility systems may be controlled by atypical receptor–ligand interactions
• Need for speed: advances in the era of high throughput interaction proteomics
• Multiple origins and functions: evolutionary pathways of HSP70 proteins in viruses
• Structures of pentatricopeptide repeat proteins
• FtsZ3 governs chloroplast division by regulating assembly and constriction of the chloroplast division machinery
• Lateral gene transfer introduced the microbial anaerobiosis-related gene rquA into early animals
• A Modular Toolkit for Nanoscale Interrogation of Multiprotein Assemblies Inside Living Cells
• DeepCodon: A deep learning codon-optimization model to enhance protein expression
• CLCC1 governs ER bilayer equilibration to maintain lipid homeostasis
• Enzyme structure correlates with variant effect predictability
• The cryo-EM structure of Photosystem I from Chromera velia with a bound superoxide dismutase heterodimer
• Chimeric mis-annotations of genes remain pervasive in eukaryotic non-model organisms
• A Single Residue Switch Controls Isomer Selectivity in the Myxobacterial Isobonnadiene Synthase
• Interactions of Wheat Powdery Mildew Effectors Involved in Recognition by the Wheat NLR PM3
• Scalable and multiplexed recorders of gene regulation dynamics across weeks
• A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform
• CCDC32 stabilizes clathrin-coated pits and drives their invagination
• ZapA uses a two‐pronged mechanism to facilitate Z ring formation in Escherichia coli
• STCRpy: a software suite for T-cell receptor structure parsing, interaction profiling, and machine learning dataset preparation
• Mechanism-guided mutagenesis of Rft1 to test its role as a dolichol-linked oligosaccharide scramblase in cells
• A Chimeric Photo-Controllable CRISPR/Cas12a System for Universal and Fast Diagnostics
• High-throughput prediction of protein–protein interactions uncovers hidden molecular networks in biosynthetic gene clusters
• AraC ‐Family Transcriptional Regulator WhpR Controls Virulence in Pseudomonas savastanoi pv. savastanoi Through Regulation of Indole Metabolism
• Phage display-mediated immuno-PCR to detect low-abundance secreted proteins in Drosophila
• Hallucinations in AlphaFold3 for Intrinsically Disordered Proteins with disorder in Biological Process Residues
• OBS-Diff: Accurate Pruning For Diffusion Models in One-Shot
• GyroSwin: 5D Surrogates for Gyrokinetic Plasma Turbulence Simulations
• Paraplume: A fast and accurate paratope prediction method provides insights into repertoire-scale binding dynamics
• Hybrid Sequential Quantum Computing
• Distilled Protein Backbone Generation
• Temporal Score Rescaling for Temperature Sampling in Diffusion and Flow Models
• NS-Pep: De novo Peptide Design with Non-Standard Amino Acids
• Small-angle X-ray scattering of engineered antigen-binding fragments: the case of glycosylated Fab from the Mannitou IgM antibody
• A new paradigm for outer membrane protein biogenesis in the Bacteroidota
• Predicting adaptive immune receptor specificities by machine learning is a data generation problem
• Modeling glycans with AlphaFold 3: capabilities, caveats, and limitations
• Flow Autoencoders are Effective Protein Tokenizers
• Marginal Flow: a flexible and efficient framework for density estimation
• AiDE-Q: Synthetic Labeled Datasets Can Enhance Learning Models for Quantum Property Estimation
• Let Physics Guide Your Protein Flows: Topology-aware Unfolding and Generation
• Is Sequence Information All You Need for Bayesian Optimization of Antibodies?
• MarS-FM: Generative Modeling of Molecular Dynamics via Markov State Models
• Gas-vacuolate Microcystis evolves cyanophage resistance under low nitrogen conditions
• The Rho guanine-nucleotide exchange factor P-Rex2 exhibits structural and regulatory features distinct from the related RhoGEF P-Rex1
• Advancing Protein Ensemble Predictions Across the Order–Disorder Continuum
• Beyond the canonical: The role of post-transcriptional regulation in drug-target interaction prediction
• FaNUDT19 contributes to 5′ cap quality control by modulating NAD+ capped RNA dynamics during strawberry fruit ripening
• The crystal structure of human transport and Golgi organization 2 homolog (TANGO2) suggests a cysteine N-terminal nucleophile (Ntn) hydrolase
• Coupled binuclear copper sites in biology: An experimentally-calibrated computational perspective
• A tetramer of BCL11A is required for stable protein production and fetal hemoglobin silencing
• Recent advances in noncanonical inhibition mechanisms of anti‐CRISPR proteins
• Bringing the genetically minimal cell to life on a computer in 4D
• Foxn3 is part of a transcriptional network that regulates primary cilia in the developing retina
• Previously Uncharacterised Aliphatic Amino Acid Positions Modulate the Apparent Catalytic Activity of the EAL Domain of ZMO₁055 and Other Cyclic Di‐ GMP‐ Specific EAL Phosphodiesterases
• Antibacterial Drug Discovery: Deep Learning Successes and Challenges through the Structural Biology Lens
• Eukaryote initiation factor 6 modulates small-cell lung carcinoma plasticity via the integrin-FAK signaling axis
• Cross-species gene redesign leveraging ortholog information and generative modeling
• Advances in synthetic biology for engineering methylotrophic microbial cell factories
• Completion of partial structures using Patterson maps with the CrysFormer machine-learning model
• VN-EGNN: E(3)- and SE(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification
• Protein language models trained on biophysical dynamics inform mutation effects
• SPOROCYTELESS/NOZZLE cooperates with MADS-domain transcription factors to regulate an auxin-dependent network controlling Megaspore-Mother-Cell differentiation
• Microbes Saving Lives and Reducing Suffering
• OsFeSOD3 Functions as an Enzymatic Component of the PEP Complex, Bifunctionally Regulating Chloroplastic ROS Metabolism and Chloroplast Biogenesis in Rice
• Assessment of Nucleic Acid Structure Prediction in CASP16
• Discovery of a novel CYP107E41 from Streptoalloteichus sp. KCCM40925 for advancing steroid hydroxylation catalysis
• Tetrameric structure of Bacillus subtilis DegQ and its predicted interaction with the DegS–DegU two-component system
• Deciphering Photosynthetic Protein Networks: A Crosslinking-MS Strategy for Studying Functional Thylakoid Membranes
• Discontinuous Epitope Fragments as Sufficient Target Templates for Efficient Binder Design
• ADAPT: Lightweight, Long-Range Machine Learning Force Fields Without Graphs
• Targeting the Membrane‐Embedded Rhomboid Protease GlpG: A Multimodal Strategy for Inhibitor Discovery and Mechanistic Insight
• Preparing for Artificial General Intelligence (AGI) in Health Professions Education: AMEE Guide No. 172
• Foundation models in plant molecular biology: advances, challenges, and future directions
• Capturing ribosomal structures in cellular extracts with cryoPRISM: A purification-free cryoEM approach reveals novel structural states
• Opportunities in proximity modulation: Bridging academia and industry
• Hidden Markov Model-Based Prokaryotic Genome Space Mining Reveals the Widespread Pervasiveness of Complex I and Its Potential Evolutionary Scheme
• Coupling chromosome organization to genome segregation in Archaea
• PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB
• hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments
• mTOR signaling governs the formation of epithelial apical projection via S6K1-RhoA and aPKC-Lgl2 axes
• Reconstitution of BNIP3/NIX-mitophagy initiation reveals hierarchical flexibility of the autophagy machinery
• Fine-scale population structure of Japanese Helicobacter pylori provides new anthropological and epidemiological insights
• An interbacterial cysteine protease toxin inhibits cell growth by targeting type II DNA topoisomerases GyrB and ParE
• Human FASTK preferentially binds single‐stranded and G‐rich RNA
• Discovery of a Two-Step Enzyme Cascade Converting Aspartate to Aminomalonate in Peptide Natural Product Biosynthesis
• Autonomous laboratories in China: an embodied intelligence-driven platform to accelerate chemical discovery
• Origin and Evolution of Bacterial Periplasmic Force Transducers
• Sequence modeling and design from molecular to genome scale with Evo
• The role of intrinsically disordered regions of SARS-CoV-2 nucleocapsid and non-structural protein 1 proteins
• Functional and Structural Characterization of Treatment-Emergent Nirmatrelvir Resistance Mutations at Low Frequencies in the Main Protease (Mpro) Reveals a Unique Evolutionary Route for SARS-CoV-2 to Gain Resistance
• Kinesin-12 POK2 polarization is a prerequisite for a fully functional division site and aids cell plate positioning
• Robust Binding Capability and Occasional Gene Loss of Telomere-Binding Proteins Underlying Telomere Evolution in Nematoda
• CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset
• On the design space between molecular mechanics and machine learning force fields
• Rational Design Principles for De Novo α-Helical Peptide Barrels with Dynamic Conductive Channels
• PARP7 as a new target for activating anti-tumor immunity in cancer
• Defense arsenal of the strict anaerobe Clostridioides difficile against reactive oxygen species encountered during its infection cycle
• Machine learning for synthetic gene circuit engineering
• Modelling and design of transcriptional enhancers
• Themis and Grb2 form a constitutive structural hub in T cell receptor signalling
• FETCH enables fluorescent labeling of membrane proteins in vivo with spatiotemporal control in Drosophila
• Foundation models in bioinformatics
• Artificial intelligence in drug development
• Cell-free protein synthesis as a method to rapidly screen machine learning-directed protease variants
• Resilience and charge-dependent fibrillation of functional amyloid: Interactions of Pseudomonas biofilm-associated FapB and FapC amyloids
• Boltz-1 Democratizing Biomolecular Interaction Modeling
• Cleavage cascade of the sigma regulator FecR orchestrates TonB-dependent signal transduction
• Similar but Distinct—Biochemical Characterization of the Staphylococcus aureus Serine Hydrolases FphH and FphI
• Rfam 15: RNA families database in 2025
• Challenge for Deep Learning: Protein Structure Prediction of Ligand-Induced Conformational Changes at Allosteric and Orthosteric Sites
• Identification of a conserved gene family with an essential role in Leishmania parasite–insect vector adhesion
• Origin and transport of bacterial hopanoids
• Discovery and characterization of a nickel enzyme family that catalyses intermolecular hydride shuttling
• Structural bioinformatic studies of eight integral transmembrane NADPH oxidases and their AlphaFold 3 predicted QTY analogs with reduced hydrophobicity
• Alphafold2 refinement improves designability of large de novo proteins
• DriftLite: Lightweight Drift Control for Inference-Time Scaling of Diffusion Models
• Learning Inter-Atomic Potentials without Explicit Equivariance
• AI for Sustainable Future Foods
• A Hierarchical Adaptive Diffusion Model for Flexible Protein-Protein Docking
• A stress-dependent TDP-43 SUMOylation program preserves neuronal function
• The future of machine learning for small-molecule drug discovery will be driven by data
• HURP regulates Kif18A recruitment and activity to synergistically control microtubule dynamics
• HIV-1 envelope glycoprotein modulates CXCR4 clustering and dynamics on the T cell membrane
• Epigenetic memory of colitis promotes tumour growth
• Machine learning-driving optimization and spatial assembly of a cell-free system for high-yield liquiritigenin production
• Metal binding site alignment enables network-driven discovery of recurrent geometries across sequence-divergent proteins and drug off-targets
• Towards sustainable freshwater systems through plant synthetic biology engineering plants for sustainability
• Plant structural biology: Emerging technologies and future biological insights
• Exploring the use of quantum computing for facilitating spatially and temporally resolved models of a biological cell
• Chloroplast glycerolipid metabolism during maintenance and under stress
• The SPARK complex forms the molecular basis of vertebrate fertilization
• The One Ring: A Monocycle Producing Class II Diterpene Cyclase from Isodon leucophyllus
• Molecular architecture of Influenza A virions
• The molecular architecture of the Arabidopsis callose synthase complex
• DNA induces non-canonical dimerization of the farnesoid X receptor
• Use of hydrogen deuterium exchange mass spectrometry in tandem with modern structural biology
• Structural and mechanistic insights into the sequential dsDNA cleavage by SpCas12f1
• Can AI Follow In Einstein's Footsteps?
• The PIN domain of SMG-5 functionally interacts with SMG-6 to stimulate NMD
• Pre-assembly of biomolecular condensate seeds drives RSV replication
• A SUMO interacting motif in the replication initiator protein of tomato yellow leaf curl virus is required for viral replication
• Exploring the Isomer Landscape, Fragment Additivity, and Vibrational Signatures of the Z-Alanine Protected Amino Acid Derivative
• Genome mining-based discovery of an atypical fungal non-reducing polyketide synthase encoding dimeric alkylresorcinol biosynthesis
• Reprogramming the GRHL2−CDK19 axis by gene therapy alleviates prostate aging
• Multiple origins, one function: evolutionary pathways of HSP70 proteins in viruses
• Metric-Guided Synthetic Image Data Rendering for Deep Learning compatible with Agentic AI
• From Observation to Insight: Mechanistic World Models and the Quest for Autonomous Discovery
• Definition and Discovery of Tandem SH3-Binding Motifs Interacting with Members of the p47phox-Related Protein Family
• Deep contrastive learning enables genome-wide virtual screening
• Protein design drives synthetic biology research of plant natural products
• Computationally-designed aptamers targeting RAD51-BRCA2 interaction impair homologous recombination and induce synthetic lethality
• A draft genome assembly of the agricultural pest Leucoptera coffeella and analysis of its dsRNA processing machinery is a key step toward RNAi-based biopesticides in Lepidoptera
• Polymerization-mediated SRFR1 condensation in upper lateral root cap cells regulates root growth
• A novel glutathione transferase harboring an FMN redox cofactor
• Modulation of host cell pathways by Coxiella burnetii Dot/Icm effectors
• Pox-AbDab: the orthopoxvirus antibody database
• A Non‐Covalent [4Fe–4S]/[2Fe] Interface in HydF Guides [FeFe]‐Hydrogenase Maturation
• Disordered N‐termini enhance the thermostability of SGNH ‐hydrolase family polyesterases
• TBK1 Induces the Formation of Optineurin Filaments That Condensate with Polyubiquitin and LC3 for Cargo Sequestration
• Pan-Angiosperm Analysis of the CLE Signaling Peptide Gene Family Unveils Paths, Patterns, and Predictions of Paralog Diversification
• Genome modeling and design across all domains of life with Evo 2
• Identification of MscS as a Key L‐Glutamate Exporter in Bacillus methanolicus
• Spread of a Single Superclone Drives Insecticide Resistance in Acyrthosiphon kondoi Across an Invasive Range
• Two OB-fold proteins from a Gram-positive conjugative element engage in relaxosome assembly and DNA processing
• Sequence-aware Prediction of Point Mutation-induced Effects on Protein-Protein Binding Affinity using Deep Learning
• On the variation of structural divergence among residues in enzyme evolution
• Apple DELLA Is Degraded Under Warm Temperature Conditions in Nicotiana benthamiana Leaves Through a COP1‐Dependent Mechanism
• Woody Host‐Specific Type III Effector HopBL2 Is Essential for Pseudomonas savastanoi Virulence and Associates With Plasmodesmata
• Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue
• Characterization of the Orphan Cytochrome P450 CYP107J1 From Bacillus subtilis Through Peroxygenase Activity Engineering
• Resource‐Dependent Metabolic and Biogeochemical Consequences of Viruses in Agricultural Soils
• Transcriptional Regulation of the Novel Theacrine Synthase Gene CsTcS2 by the CsTINY–CsWRKY33 Module Underpins Theacrine Biosynthesis in Camellia sinensis
• Quantum Biology Using Ultrafast Integrative and Molecular Engineering Tools: A Perspective
• AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network
• Structural study of Nicotiana benthamiana NADPH-dependent thioredoxin reductase C and its molecular mechanism of interaction with 2-Cys peroxiredoxin
• In Silico Analysis of Potential Stabilizer Binding Sites at Protein–RNA Interfaces
• Lubricin’s Mucin Domain Has Strong Polyproline Type II Helical Character
• Cooperative reading of DECA-CCAAT composite element by the TALE/NF-Y/Sp2 transcription factors
• A new macromolecular crystallography endstation at NanoTerasu for accelerating structural biology and drug discovery
• Retrograde signaling is required for Slm35-mediated negative regulation of mitophagy in yeast
• Characterisation of a Novel Jumbo Lytic Aeromonas dhakensis Bacteriophage P19 and Its Endolysin
• Covalent targeting of PSMD14 by Eupalinolide B induces oncoprotein degradation and apoptosis in acute promyelocytic leukemia cells
• Crystal structure of Methanococcus jannaschii dihydroorotase with substrate bound
• The interplay between the pyramidalization of carbonyl carbons and the n → π* interactions in biomolecules
• Investigating the role of a conserved hydrophobic pocket of gp41 in the anti‐ HIV activity of fusion inhibitors
• Dynamic disorder is crucial for mitochondrial protein import
• Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence
• Unraveling circadian rhythms—computational insights into molecular mechanisms
• EcDNA-borne structural variants drive oncogenic fusion transcript amplification
• RNA-triggered Cas12a3 cleaves tRNA tails to execute bacterial immunity
• In situ structure of a gap junction–stomatin complex
• Differential PaxillinB dynamics at Dictyostelium cell-substrate adhesions
• PLM-interact: extending protein language models to predict protein-protein interactions
• Building an expanded bio-based economy through synthetic biology
• Genetic control of morphological transitions in a coacervating protein template
• EPLINα controls integrin recycling from Rab21 endosomes to drive breast cancer cell migration
• KLF5 enables dichotomous lineage programs in pancreatic cancer via the AAA+ ATPase coactivators RUVBL1 and RUVBL2
• MmpL12 transports lipooligosaccharides and impacts virulence in Mycobacterium marinum
• Structural basis of G6P/Pi transport and inhibition in SLC37A4
• Avirulence depletion assay: Combining R gene-mediated selection with bulk sequencing for rapid avirulence gene identification in wheat powdery mildew
• Tandem Duplications in UBTF Create XPO1-Dependent Nuclear Export Signals that Reveal a Leukemic Therapeutic Dependency
• Characterisation of a Self‐Sufficient Cytochrome P450 Enzyme From the Bacterium Thermosporothrix hazakensis and Its Conversion Into a Peroxygenase
• Replacement of a single residue in an antibody abolishes cognate antigen binding, as predicted by theoretical methods
• Structural and functional characterization of human sweet taste receptor
• A hypomorphic model of CPS1 deficiency for investigating the effects of hyperammonemia on the developing nervous system
• Domain-substituted IGF2 tag modulates targeting of lentiviral gene therapy for Hunter syndrome
• TBM preferred to AlphaFold 3 for functional models of insect odorant receptors
• A STING-CASM-GABARAP Pathway Activates LRRK2 at Lysosomes
• Pirin, a redox-sensitive modulator of beta-oxidation, generates hydroxyl radicals and interacts with CatR, the transcriptional repressor of the major vegetative catalase gene in Streptomyces
• Mycobacterium tuberculosis sulfurtransferase SseA is activated by its neighboring gene product Rv3284
• Computational nanobody design through deep generative modeling and epitope landscape profiling
• Bridging prediction and reality: Comprehensive analysis of experimental and AlphaFold 2 full-length nuclear receptor structures
• Lessons from complex systems science for AI governance
• Inhibition of Clostridioides difficile- specific DNA adenine methyltransferase CamA by analogs of S -adenosyl-L-methionine
• A conserved nuclease facilitates environmental DNA uptake
• From genes to function: regulation, maturation, and evolution of cytochrome c nitrite reductase in nitrate reduction to ammonium
• RinRK1's extracellular domain acts as a host‐specific gatekeeper for rhizobial infection in Medicago truncatula
• EZpred: improving deep learning-based enzyme function prediction using unlabeled sequence homologs
• An Interbacterial Cysteine Protease Toxin Inhibits Cell Growth by Targeting Type II DNA Topoisomerases GyrB and ParE
• AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications
• Gener anno : A Genomic Foundation Model for Metagenomic Annotation
• SSAlign: Ultrafast and Sensitive Protein Structure Search at Scale
• Manganese handling in plants: Advances in the mechanistic and functional understanding of transport pathways
• Natural Design of a Stabilized Cross‐β Fold: Structure of the FuA FapC from Pseudomonas Sp. UK4 Reveals a Critical Role for Stacking of Imperfect Repeats
• CCDC32 stabilizes clathrin-coated pits and drives their invagination
• In vivo multiplex imaging of dynamic neurochemical networks with designed far-red dopamine sensors
• Bacterial peptide deformylase inhibitors induce prophages in competitors
• All-at-once RNA folding with 3D motif prediction framed by evolutionary information
• Structural dynamics between Argonaute-2 and CK1α promote target RNA release in microRNA-mediated silencing
• The solute carrier superfamily interactome
• Descriptive power and predictive limits of a discrete Hasimoto--DNLS model of protein backbone structure
• The crystal structure of an uncharacterized domain of P113 from Plasmodium falciparum
• Design principles of cell-state-specific enhancers in hematopoiesis
• Protein design accelerates the development and application of optogenetic tools
• Protein editing using a coordinated transposition reaction
• Massive experimental quantification allows interpretable deep learning of protein aggregation
• Development of DNA Aptamers Against Leishmania infantum GP63 Protein for Therapeutic and Diagnostic Applications
• The multiple roles of the NlpC_P60 peptidase family in mycobacteria – an underexplored target for antimicrobial drug discovery
• Measuring Mid-2025 LLM-Assistance on Novice Performance in Biology
• Activity-based protein profiling reveals both canonical and novel ubiquitin pathway enzymes in Plasmodium
• Evaluation of predictions of disordered binding regions in the CAID2 experiment
• The role of ladderlectin in spermatogenesis and ovarian sperm storage in the black rockfish (Sebastes schlegelii)
• Oligomerised RIPK1 is the main core component of the CD95 necrosome
• Conformational analysis of biomineral proteins interacting with inorganic minerals using dispersive mineral particles for solution NMR
• Structure of the Calvin-Benson-Bassham sedoheptulose-1,7-bisphosphatase from the model microalga Chlamydomonas reinhardtii
• Computational drug repurposing: approaches, evaluation of in silico resources and case studies
• Lipid-mediated mechanism of drug extrusion by a heterodimeric ABC exporter
• HIV-1 broadly neutralizing antibodies demonstrate a high propensity for binding to heme
• Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls
• Slice'N'Dice : maximizing the value of predicted models for structural biologists
• Tonic ubiquitination of the central body weight regulator melanocortin receptor 4 (MC4R) promotes its constitutive exit from cilia
• AI: A transformative opportunity in cell biology
• Deep learning and generative artificial intelligence in aging research and healthy longevity medicine
• Do the Shuffle: Expanding the Synthetic Biology Toolkit for Shufflon-like Recombination Systems
• Annotation Vocabulary (Might Be) All You Need
• A CDK1 phospho-switch reprograms TRAIP to unload replisomes in mitosis
• AI-predicted protein deformation encodes energy landscape perturbation
• Metabolite glues as a means of purine sensing and chemotherapeutic response
• Cdc42 and Rac2 act through the formin-like Frl/FMNL to control lamellocyte shape and encapsulation of parasitoid wasp eggs in Drosophila
• A distinctive PDZ:β-hairpin interaction mediates AFDN complex with SCRIB and promotes binding to KRAS
• Dynamic anatomy of the replisome under stress
• Derlin-like proteins are essential for the function of Euglena gracilis chloroplasts
• The structural chemistry and biosynthesis of chlorophylls
• Cross-reactive CD4+ T cell responses towards seasonal and avian influenza
• Polyethylene Glycol Induced Condensation Leads to an Anomalous FRET Response from a Flexible Linker-Fluorescent Protein Crowding Sensor
• FaRIF as a key regulator of strawberry fruit ripening: deciphering its targets and interaction networks
• Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysical Structural Invariance, Confidence Failures, and Concerns for Protein Design
• G protein–coupled receptor kinase 3 couples atypical chemokine receptor 4 independent of G proteins
• Tools For Building Artificial Biological Nanostructures
• Transition-state analysis of the arginine-specific human ADP-ribosyltransferase 1
• Decoding the Grammar of Protein-Protein Interaction Interfaces with Multimodal Representations
• Assessment of Alphafold Protein Models for Small-Molecule Ligand Docking versus Co-Folding
• Modular teaching for interdisciplinary education: Insights from a course in industrial biotechnology for lignocellulose-based processes
• DNAM-1 mediates NK-cell activation and host-pathogen interaction via direct binding to fungal cell wall proteases
• Affinity-matured B cell responses neutralizing type-I interferons underlie severe viral infections
• P450 Cyptide Synthase AscB Catalyzes Fused Cyclophane at the YxWxH Motif on the Precursor Peptides
• Characterization of VQ Gene Family and Its Roles in Anthracnose Stress Responses of Juglans regia
• The Influence of Ligands on AlphaFold3 Prediction of Cryptic Pockets
• The Synthetic Epitope Atlas: High-Throughput Design and Validation of De Novo Antibody-Antigen Complexes
• Dual-ActionTetrapeptide Analogue of PsychrophilicFungal Origin: Potent Inhibitor of Human Nicotinic Acetylcholine Receptorswith Antinociceptive and Muscle-Relaxant Activity
• Evaluating zero‐shot prediction of monomeric protein design success by AlphaFold , ESMFold , and ProteinMPNN
• Engineering of genetically encoded programmable calcium channel inhibitory binders
• Discovery, design, and engineering of enzymes based on molecular retrobiosynthesis
• LUCID: An Integrative Approach for Target Discovery and dsRNA Design in Plant Fungal Pathogens
• Defensomes, counter-defensomes, and the remodeling of microbial communities
• Structures of nucleotide-bound Redondovirus Rep protein link conformation and function
• RET receptor tyrosine kinase architecture, assemblies, and activation
• Algebraic Approach to Ridge-Regularized Mean Squared Error Minimization in Minimal ReLU Neural Network
• Plant Kelch phosphatases are Ser/Thr phosphatases involved in cell cycle regulation
• High-Affinity Protein Binder Design via Flow Matching and In Silico Maturation
• Impact de l’intelligence artificielle sur la production, la transformation, la distribution et les échanges agroalimentaires : l’expérience française dans un contexte européen
• Multi-domain Distribution Learning for De Novo Drug Design
• RemoteFoldSet: Benchmarking Structural Awareness of Protein Language Models
• FRET-guided selection of RNA 3D structures
• AI-based Methods for Simulating, Sampling, and Predicting Protein Ensembles
• A review of topological data analysis and topological deep learning in molecular sciences
• From Prediction to Understanding: Will AI Foundation Models Transform Brain Science?
• Securing the Language of Life: Inheritable Watermarks from DNA Language Models to Proteins
• Boltzina: Efficient and Accurate Virtual Screening via Docking-Guided Binding Prediction with Boltz-2
• Use of translational fusions to express functional Klebsiella oxytoca dinitrogenase reductase in plant mitochondria
• White-box machine learning for uncovering physically interpretable dimensionless governing equations for granular materials
• De novo Design of All-atom Biomolecular Interactions with RFdiffusion3
• Foam-Agent 2.0: An End-to-End Composable Multi-Agent Framework for Automating CFD Simulation in OpenFOAM
• ProFusion: 3D Reconstruction of Protein Complex Structures from Multi-view AFM Images
• ProTDyn: a foundation Protein language model for Thermodynamics and Dynamics generation
• Synthetic Protein-Ligand Complex Generation for Deep Molecular Docking
• Adding a twist to the loops: the role of DNA superhelicity in the organization of chromosomes by SMC protein complexes
• The Marchantia polymorpha recombinase MpRAD51 is at the crossroads of morphogenesis and the DNA damage response
• Protein‐ RNA Docking Benchmark v3.0 Integrated With Binding Affinity
• Uridine-sensitized screening identifies demethoxy-coenzyme Q and NUDT5 as regulators of nucleotide synthesis
• Neuromorphic Intelligence
• Loss and Gain of Aqp10 Paralogs With Broad Solute Selectivity in Anguillid Eels
• Host-Specific Adaptation of Legionella pneumophila to Single and Multiple Hosts
• Programmable 200 GOPS Hopfield-inspired photonic Ising machine
• IR Spectroscopic Studies of Gas-Phase Peptides
• Solve it with EASE
• Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications
• Hyperbolic Large Language Models
• Evaluation of De Novo Deep Learning Models on the Protein-Sugar Interactome
• INGRID: Intelligent Generative Robotic Design Using Large Language Models
• SafeProtein: Red-Teaming Framework and Benchmark for Protein Foundation Models
• Scale-Adaptive Generative Flows for Multiscale Scientific Data
• Categorizing prediction modes within low-pLDDT regions of AlphaFold 2 structures: near-predictive, pseudostructure and barbed wire
• Fe( ii ) and 2-oxoglutarate-dependent dioxygenases for natural product synthesis: molecular insights into reaction diversity
• Relative Trajectory Balance is equivalent to Trust-PCL
• Learning residue level protein dynamics with multiscale Gaussians
• OTMol: Robust Molecular Structure Comparison via Optimal Transport
• Identifying and characterizing a missing peroxin—PEX8—in Arabidopsis thaliana
• Resilient Biosecurity in the Era of AI-Enabled Bioweapons
• Controllable 3D Molecular Generation for Structure-Based Drug Design Through Bayesian Flow Networks and Gradient Integration
• Genomic adaptations for tail-length evolution in arboreal snakes
• Boltz-ABFE: Free Energy Perturbation without Crystal Structures
• GRADSTOP: Early Stopping of Gradient Descent via Posterior Sampling
• Sparse Autoencoders for Low-N Protein Function Prediction and Design
• Bioinformatic discovery of type 11 secretion system (T11SS) cargo across the Proteobacteria
• Amortized Sampling with Transferable Normalizing Flows
• Deep learning applications advance plant genomics research
• Engineered orthogonal translation systems from metagenomic libraries expand the genetic code
• Sesame: Opening the door to protein pockets
• Improved structure of mouse gasdermin D: a new blueprint for structure-based drug design
• Molecular representation learning: cross-domain foundations and future Frontiers
• Black-box optimization in immunology and beyond: A practical guide to algorithms and future directions
• A SlEIN2 ‐centered epigenetic network equilibrates fruit ripening and innate immunity in tomato
• Microbial Cell Factories in the Bioeconomy Era: From Discovery to Creation
• NanoDel: Identification of large-scale mitochondrial DNA deletions using long-read sequencing
• Protein Set Transformer: a protein-based genome language model to power high-diversity viromics
• CluSeek: Bioinformatics Tool to Identify and Analyze Gene Clusters
• Antigen-agnostic identification of poxvirus broadly neutralizing antibodies targeting OPG153
• Understanding domain swapping in the c-Src SH3 domain through hinge-loop mutagenesis
• CASP16 Protein Monomer Structure Prediction Assessment
• NucEL: Single-Nucleotide ELECTRA-Style Genomic Pre-training for Efficient and Interpretable Representations
• A Dataset for Distilling Knowledge Priors from Literature for Therapeutic Design
• Considering the ethics of large machine learning models in the chemical sciences
• Exploring Quantum Annealing for Coarse-Grained Protein Folding
• Energy-Based Models for Predicting Mutational Effects on Proteins
• Hydrophobic residues in the α‐synuclein NAC domain drive seed‐competent fibril formation and are targeted by peptide inhibitors
• Highlights of Model Quality Assessment in CASP16
• In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies
• Development of visible light‐sensitive human neuropsin ( OPN5 ) via single amino acid substitution
• Single-cell structural biology with intracellular electron crystallography
• Moss BRCA2 lacking canonical DNA binding domain promotes efficient homologous recombination and binds to DNA
• Evolution and diversity of oxidoreductases involved in redox balance and energy conservation
• Genomic analysis of Ostreococcus tauri -infecting viruses reveals a hypervariable region associated with host–virus interactions
• DeepFold-PLM: accelerating protein structure prediction via efficient homology search using protein language models
• A dual-factor complex governs archaeal ribosome hibernation by sensing energy status
• High-accuracy protein complex structure modeling based on sequence-derived structure complementarity
• S9 protease WprP2 catalyzes uniform cleavage on the precursor peptide in RiPP biosynthesis
• The novel ITPR1 p.Phe2566Ser variant impairs IP 3 R1‐mediated Ca 2+ release and is associated with ataxia and miosis
• Mrx6 binds the Lon protease Pim1 N-terminal domain to confer selective substrate specificity and regulate mtDNA copy number
• Learning the language of protein-protein interactions
• The Arabidopsis TIRome informs the design of artificial TIR (Toll/interleukin-1 receptor) domain proteins
• MAVISp: A Modular Structure-Based Framework for Protein Variant Effects
• In Silico Analysis of Protease Inhibitors in Three Solanaceous Crops Identifies Potential Candidates for Phytopathogen and Plant Pest Management
• AlphaFold reveals but sometimes distorts an organizational principle of protein folding
• FrustraMPNN: An ultra-fast deep learning tool for proteome-scale analysis of deep mutational single-residue local energetic frustration in proteins
• A New Insight into the Study of Neural Cell Adhesion Molecule (NCAM) Polysialylation Inhibition Incorporated the Molecular Docking Models into the NMR Spectroscopy of a Crucial Peptide–Ligand Interaction
• Designing de novo TIM Barrels: Insights into Stabilization, Diversification, and Functionalization Strategies
• FlowBack-Adjoint: Physics-Aware and Energy-Guided Conditional Flow-Matching for All-Atom Protein Backmapping
• An Auditable Agent Platform For Automated Molecular Optimisation
• MD-LLM-1: A Large Language Model for Molecular Dynamics
• Fidelity, specialization, and evolution of Paramecium PolX DNA polymerases involved in programmed double-strand break DNA repair
• Evaluating Use of Generative Artificial Intelligence in Clinical Pathology Practice: Opportunities and the Way Forward
• Multi-state Protein Design with DynamicMPNN
• Reducing Data Requirements for Sequence-Property Prediction in Copolymer Compatibilizers via Deep Neural Network Tuning
• Thiol post-translational modifications modulate allosteric regulation of the OpcA-G6PDH complex through conformational gate control
• From genes to Black Rust: genomic insights into corrosive methanogens
• Computational approaches for RNA structure prediction and design
• Sequence-based protein-protein interaction prediction and its applications in drug discovery
• Programmable Virtual Humans Toward Human Physiologically-Based Drug Discovery
• Latent-X: An Atom-level Frontier Model for De Novo Protein Binder Design
• A fully automated benchmarking suite to compare macromolecular complexes
• Enigma: An Efficient Model for Deciphering Regulatory Genomics
• Pneumococcal S protein coordinates cell wall modification and repair to resist host antimicrobials
• n P-Collabs: Investigating Counterion-Mediated Bridges in the Multiply Phosphorylated Tau-R2 Repeat
• The SUbventral-Gland Regulator (SUGR-1) of nematode virulence
• eIF2Bε phosphorylation activates integrated stress response-mediated protein translation and links stress signalling to amyloidogenesis in Alzheimer’s disease
• Winter‐active spiders ( Clubiona ) have a hyperactive antifreeze protein with a unique beta‐solenoid fold
• Transcriptome-wide profiling of alternative splicing regulators with CRISPore-seq
• ProteinSight: A Volumetric Deep Learning Model for Carotenoid-Binding Site Prediction
• TRAMbio: a flexible python package for graph rigidity analysis of macromolecules
• Dissimilar Reactions and Enzymes for Psilocybin Biosynthesis in Inocybe and Psilocybe Mushrooms
• A structure-guided approach to non-coding variant evaluation for transcription factor binding using AlphaFold 3
• Natural variation in IBF1 disrupts its interaction with CHS1 and affects metabolism of hulls in rice
• Ultra-rare biallelic THAP12 variants cause loss of function and underlie severe epileptic encephalopathy
• Bimodal retrograde signaling disrupts a suppressor network and activates a key transcriptional activator to direct stress responses
• Mechanism-based inhibition of zinc-dependent histone deacetylases
• De novo acyl carrier proteins display structure-independent modification and sequence novelty
• Guided tour through the small protein landscape of Methanosarcina mazei using proteomics and biochemical approaches
• Dynamic Lysine Acetylation Disrupts Isocitrate Lyase Function and Enables Metabolic Optimisation
• DcH3.3 and DcNAC1 Regulate the Expression of UGT73A93 Involved in the Changes in Flower Colour and Fungal Resistance in Carnation
• Redundant Glycerol‐3‐Phosphate Acyltransferases Regulate Thermo‐Sensitive Genic Male Sterility in Rice
• A universal polyphosphate kinase powers in vitro transcription
• Engineering an AlkS ‐ PalkB Transcription Factor‐Based Biosensor With Improved Sensitivity to Isobutanol and Other Short‐Chain Alcohols
• Rational design of gold nanoparticles functionalized with aptamers for improved West Nile virus detection
• A single nucleotide mutation of BnaC05.POLIB creates yellow-white chimeric flower in Brassica napus
• Amino acid homorepeats act as buffers to maintain proteostasis and constrain the compatible sequence space of proteomes
• Heterologous expression and functional characterization of two alginate lyases in corynebacterium glutamicum
• Molecular Glue Degraders Redefining Targeted Therapies From Discovery to Therapeutic Applications
• Applications of modular co-design for de novo 3D molecule generation
• Heterochromatome wide analyses reveal MBD2 as a phase separation scaffold for heterochromatin compartmentalization and composition
• Pan-prediction of major histocompatibility complex class II–restricted epitopes across species via an AlphaFold-based quantification scheme
• A computational workflow for predicting protein oligomer complex structure induced by small-molecule PPI modulators: validation with BMS-1166 induced PD-L1 Homodimers
• Mutations within the predicted fragment-binding region of FAM83G/SACK1G abolish its interaction with the Ser/Thr kinase CK1α
• Exploiting the synergy between computational and experimental biophysics for efficient cancer drug development
• Preparation of soluble and functional recombinant HTLV-1 Tax protein using bacterial chaperones
• Systematic structure-based analysis of RET variants in MEN2A and Hirschsprung's disease, and the paradoxical co-occurrence of both conditions
• K-Search: LLM Kernel Generation via Co-Evolving Intrinsic World Model
• Benchmarking datasets for machine learning in protein function prediction
• Flow Matching Meets Biology and Life Science: A Survey
• A Comprehensive Review of Transformer-based language models for Protein Sequence Analysis and Design
• Unconventional CD8 + T cell surveillance of cytomegalovirus via Qa-1/HLA-E–restricted epitope recognition
• Predicting and Designing Red Fluorescent Protein Variants Using Sequence-to-Function Machine Learning Models
• Functional characterization of key enzymes involved in the biosynthesis of distinctive flavonoids and stilbenoids in Morus notabilis
• QOBRA: A Quantum Operator-Based Autoencoder for De Novo Molecular Design
• Benchmarking AlphaFold3's protein-protein complex accuracy and machine learning prediction reliability for binding free energy changes upon mutation
• Protenix-Mini: Efficient Structure Predictor via Compact Architecture, Few-Step Diffusion and Switchable pLM
• SynCoGen: Synthesizable 3D Molecule Generation via Joint Reaction and Coordinate Modeling
• TRAF2 binds to TIFA via a novel motif and contributes to its autophagic degradation
• The calcineurin pathway regulates extreme thermotolerance, cell membrane and wall integrity, antifungal resistance, and virulence in Candida auris
• Chain-length regulation by WzzE is necessary for, but genetically separable from, cyclic enterobacterial common antigen synthesis
• DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders
• The ER–PM interaction is essential for cytokinesis and recruits the actin cytoskeleton through the SCAR/WAVE complex
• Functional characterization of the Csm1-like protein TITAN 9 in Arabidopsis thaliana
• Protein structure prediction and design for high-throughput computing
• How did we get there? AI applications to biological networks and sequences
• Towards a comprehensive view of the pocketome universe – biological implications and algorithmic challenges
• Snapshot of in-cell protein contact sites reveals new host factors and hijacking of paraspeckles during influenza A virus infection
• Disruption of SETD 3‐mediated histidine‐73 methylation by the BWCFF ‐associated β‐actin G 74 S mutation
• CTCF binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientation
• Chemometric modeling, inverse docking, and molecular simulations-driven design for multilayered prioritization of novel leishmanicidal agents based on a 2-aminobenzimidazole scaffold
• A novel modulator of IL-6R prevents inflammation-induced preterm birth and improves newborn outcome
• CCDC32 stabilizes clathrin-coated pits and drives their invagination
• Structural insights into the binding of human TGIF1 with SMAD2 MH2 domain
• Current AI technologies in cancer diagnostics and treatment
• Start right to end right: authentic open reading frame selection matters
• Discovery of iridoid cyclase completes the iridoid pathway in asterids
• Asp/ASPM phospho-regulation throughout the cell cycle
• Structural basis for OAS2 regulation and its antiviral function
• AlphaFold Database Debiasing for Robust Inverse Folding
• SToFM: a Multi-scale Foundation Model for Spatial Transcriptomics
• SuperMetal: a generative AI framework for rapid and precise metal ion location prediction in proteins
• HEIMDALL: a grapH-based sEIsMic Detector And Locator for microseismicity
• Dynamic data generation and dynamic portfolio selection: an application of a score-based diffusion model
• Efficient Molecular Conformer Generation with SO(3)-Averaged Flow Matching and Reflow
• La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching
• Geometric Generative Modeling with Noise-Conditioned Graph Networks
• Defining the Antitumor Mechanism of Action of a Clinical-stage Compound as a Selective Degrader of the Nuclear Pore Complex
• evo3D R package: a spatial haplotype framework for structure-informed analysis of molecular evolution
• Learning Diffusion Models with Flexible Representation Guidance
• AMix-1: A Pathway to Test-Time Scalable Protein Foundation Model
• Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins
• Unavailability of experimental 3D structural data on protein folding dynamics and necessity for a new generation of structure prediction methods in this context
• Can AI-predicted complexes teach machine learning to compute drug binding affinity?
• Machine Learning-Driven Enzyme Mining: Opportunities, Challenges, and Future Perspectives
• Best Practices for Machine Learning-Assisted Protein Engineering
• MODA: A Unified 3D Diffusion Framework for Multi-Task Target-Aware Molecular Generation
• A multilayered network reveals the centrality of newly discovered Nucleocytoviricota in wastewater treatment plant communities
• A Malliavin calculus approach to score functions in diffusion generative models
• Predicting mutational effects on protein binding from folding energy
• PRING: Rethinking Protein-Protein Interaction Prediction from Pairs to Graphs
• Quaternionic Response Geometry for Proteins: Toward a Noncommutative Theory of Ordered Deformations
• Domain architecture of plant eukaryotic translation initiation factor 3 subunit E governs interaction with translational cis -elements to regulate pollen tube growth
• All-atom inverse protein folding through discrete flow matching
• Quantum Algorithm for the Fixed-Radius Neighbor Search
• QuickBind: A Light-Weight And Interpretable Molecular Docking Model
• Position: A Theory of Deep Learning Must Include Compositional Sparsity
• HelixDesign-Antibody: A Scalable Production-Grade Platform for Antibody Design Built on HelixFold3
• IntFold: A Controllable Foundation Model for General and Specialized Biomolecular Structure Prediction
• Information encoding in spherical DFT
• BoltzNCE: Learning Likelihoods for Boltzmann Generation with Stochastic Interpolants and Noise Contrastive Estimation
• Iterative Distillation for Reward-Guided Fine-Tuning of Diffusion Models in Biomolecular Design
• HelixPipe: Efficient Distributed Training of Long Sequence Transformers with Attention Parallel Pipeline Parallelism
• The balancing act between lipid droplets and lysosomes for membrane functionality in age-related neurodegeneration and inflammation
• _sampleworks:_ A Modular Platform for Experimentally Guided Biomolecular Ensemble Generation
• TABASCO: A Fast, Simplified Model for Molecular Generation with Improved Physical Quality
• Characterisation of the thermophilic P450 CYP116B305 identified using metagenomics-derived sequence data from an Australian hot spring
• Computational methods for modeling protein–protein interactions in the AI era: Current status and future directions
• How AI agents will change cancer research and oncology
• Enzymatic combinatorial synthesis of E-64 and related cysteine protease inhibitors
• Somatic PIK3R1 mutations in the iSH2 domain are accessible to PI3Kα inhibition
• GPU-accelerated homology search with MMseqs2
• Uncovering Microbial Biosynthetic Potential with Genomic Context-aware Protein Language Model
• Unequally Abundant Chromosomes and Unusual Collections of Transferred Sequences Characterize Mitochondrial Genomes of Gastrodia (Orchidaceae), One of the Largest Mycoheterotrophic Plant Genera
• Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls
• Structures of Legionella pneumophila serogroup 1 peptide deformylase bound to nickel(II) and actinonin
• A Quantum Framework for Protein Binding-Site Structure Prediction on Utility-Level Quantum Processors
• QDockBank: A Dataset for Ligand Docking on Protein Fragments Predicted on Utility-Level Quantum Computers
• Droplet growth, Ostwald's rule, and emergence of order in Fused in Sarcoma
• CovDocker: Benchmarking Covalent Drug Design with Tasks, Datasets, and Solutions
• Large Language Model Agent for Modular Task Execution in Drug Discovery
• Unraveling the Potential of Diffusion Models in Small Molecule Generation
• Ubiquitin-dependent proteolysis of KNL2 driven by APC/CCDC20 is critical for centromere integrity and mitotic fidelity
• Accept More, Reject Less: Reducing up to 19% Unnecessary Desk-Rejections over 11 Years of ICLR Data
• Position: Intelligent Science Laboratory Requires the Integration of Cognitive and Embodied AI
• Toward the Explainability of Protein Language Models
• Operator Forces For Coarse-Grained Molecular Dynamics
• MegaFold: Efficient Training of Next-Generation 3D Attention Protein Models on Cross-Platform GPUs
• The accessory adapters FAF1, FAF2, and UBXN7 accelerate proteasomal degradation by increasing prior p97-mediated substrate unfolding
• Cryo-EM and single molecule visualization unravel the role of human condensin II activation by M18BP1 in driving DNA compaction
• Loss‐of‐function coding variants in the Ras of complex proteins/ GTPase domain of leucine rich repeat kinase 2
• AbRank: A Benchmark Dataset and Metric-Learning Framework for Antibody-Antigen Affinity Ranking
• Assessing small molecule conformational sampling methods in molecular docking
• Diffusion Sequence Models for Enhanced Protein Representation and Generation
• Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings
• Leveraging Influence Functions for Resampling Data in Physics-Informed Neural Networks
• Geometric deep learning assists protein engineering. Opportunities and Challenges
• Conserved hinge regions in SYMRK enable release of malectin-like domain for symbiont passage during rhizobia-legume symbiosis
• Category-based Galaxy Image Generation via Diffusion Models
• A trypanosome-specific complex mediates late-stage processing of cytosolic LSU rRNA
• Sampling 3D Molecular Conformers with Diffusion Transformers
• ProteinZero: Self-Improving Protein Generation via Online Reinforcement Learning
• DISPROTBENCH: Uncovering the Functional Limits of Protein Structure Prediction Models in Intrinsically Disordered Regions
• Lightweight MSA Design Advances Protein Folding From Evolutionary Embeddings
• DisProtEdit: Exploring Disentangled Representations for Multi-Attribute Protein Editing
• HPC-AI Coupling Methodology for Scientific Applications
• Curriculum Learning for Biological Sequence Prediction: The Case of De Novo Peptide Sequencing
• AlphaEvolve: A coding agent for scientific and algorithmic discovery
• Chaos, coherence and turbulence
• Graph Neural Networks in Modern AI-aided Drug Discovery
• BSA: Ball Sparse Attention for Large-scale Geometries
• Spectra-to-Structure and Structure-to-Spectra Inference Across the Periodic Table
• Holistic approach and Advanced Color Singlet Identification for physics measurements at high energy frontier
• PPDiff: Diffusing in Hybrid Sequence-Structure Space for Protein-Protein Complex Design
• SIMSHIFT: A Benchmark for Adapting Neural Surrogates to Distribution Shifts
• How to build the virtual cell with artificial intelligence: Priorities and opportunities
• The intracellular domain of TLR2 is capable of high‐affinity Zn binding: possible outcomes for the receptor activation
• Refining the Na V 1 .7 pharmacophore of a class of venom‐derived peptide inhibitors via a combination of in silico screening and rational engineering
• MKFGO: Integrating Multi-Source Knowledge Fusion with Pre-Trained Language Model for High-Accuracy Protein Function Prediction
• Novel atypical thioredoxins with potential redox activity in eukaryote photosynthetic organisms
• Transcriptional Dynamics Uncover the Role of BNIP3 in Mitophagy during Muscle Remodeling in Drosophila
• Characterisation of the Self‐Sufficient Cytochrome P450 CYP116B234 From Rhodococcus globerulus and Its Suggested Native Role in 2‐Hydroxyphenylacetic Acid Metabolism
• Characterization and comparison of temperature-sensitive Schizosaccharomyces pombe mutants of the septation initiation network scaffolds, Cdc11 and Sid4
• Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins
• Large scale prospective evaluation of co-folding across 557 Mac1-ligand complexes and three virtual screens
• Tryptoline Stereoprobe Elaboration Identifies Inhibitors of the GRPEL1-HSPA9 Chaperone Complex
• AQUATIC-Diff: Additive Quantization for Truly Tiny Compressed Diffusion Models
• How ascorbate tunes the activity and substrate selectivity of Fe(II)-dependent dioxygenase superfamily enzymes
• UniPTMs: The First Unified Multi-type PTM Site Prediction Model via Master-Slave Architecture-Based Multi-Stage Fusion Strategy and Hierarchical Contrastive Loss
• Assembly and the gating mechanism of the Pel exopolysaccharide export complex PelBC of Pseudomonas aeruginosa
• ProtMamba: a homology-aware but alignment-free protein state space model
• Dynamic Location Search for Identifying Maximum Weighted Independent Sets in Complex Networks
• A SynBio explosion: a whole new world for Rubisco engineering
• The Effects of Rapid Mitochondrial Gene Loss on Organellar Proteomes
• Multiscale guidance of protein structure prediction with heterogeneous cryo-EM data
• Protein Inverse Folding From Structure Feedback
• Polyketide synthase-derived sphingolipids mediate microbiota protection against a bacterial pathogen in C. elegans
• UniSite: The First Cross-Structure Dataset and Learning Framework for End-to-End Ligand Binding Site Detection
• ProtInvTree: Deliberate Protein Inverse Folding with Reward-guided Tree Search
• Look mom, no experimental data! Learning to score protein-ligand interactions from simulations
• Aligning Protein Conformation Ensemble Generation with Physical Feedback
• State-aware protein-ligand complex prediction using AlphaFold3 with purified sequences
• Improving Protein Sequence Design through Designability Preference Optimization
• CryoCCD: Conditional Cycle-consistent Diffusion with Biophysical Modeling for Cryo-EM Synthesis
• Representing local protein environments with machine learning force fields
• Machine-Learned Potentials for Solvation Modeling
• GeneBreaker: Jailbreak Attacks against DNA Language Models with Pathogenicity Guidance
• The informativeness of the gradient revisited
• HelixDesign-Binder: A Scalable Production-Grade Platform for Binder Design Built on HelixFold3
• Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling
• BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design
• Molecular characterization and immunoinformatics-based design of a multi-epitope vaccine against Staphylococcus nepalensis
• Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction
• Deep Active Inference Agents for Delayed and Long-Horizon Environments
• Machine learning in NMR spectroscopy
• CreoPep: A Universal Deep Learning Framework for Target-Specific Peptide Design and Optimization
• How to build a consistency model: Learning flow maps via self-distillation
• AbBiBench: A Benchmark for Antibody Binding Affinity Maturation and Design
• Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing
• Applications of Modular Co-Design for De Novo 3D Molecule Generation
• ConfRover: Simultaneous Modeling of Protein Conformation and Dynamics via Autoregression
• Flexible MOF Generation with Torsion-Aware Flow Matching
• Open and Sustainable AI: challenges, opportunities and the road ahead in the life sciences (October 2025 -- Version 2)
• Can Large Language Models Design Biological Weapons? Evaluating Moremi Bio
• Tuning the interaction of a ParA-type ATPase with its partner separates bacterial organelle positioning from partitioning
• Virtual Cells: Predict, Explain, Discover
• Scalable Autoregressive 3D Molecule Generation
• Integrating computational detection and experimental validation for rapid GFRAL-specific antibody discovery
• Predicting metal-protein interactions using cofolding methods: Status quo
• Discovery of molecular glues by modeling ternary complex conformational ensembles and thermodynamic stability
• LaPON: A Lagrange's-mean-value-theorem-inspired operator network for solving PDEs and its application on NSE
• Computational prediction resolves thousands of homooligomeric phage protein structures
• AI-Driven Automation Can Become the Foundation of Next-Era Science of Science Research
• FlashBias: Fast Computation of Attention with Bias
• VenusX: Unlocking Fine-Grained Functional Understanding of Proteins
• Advances in the field of RNA 3D structure prediction and modeling, with purely theoretical approaches, and with the use of experimental data
• SurfDock is a surface-informed diffusion generative model for reliable and accurate protein–ligand complex prediction
• Democratizing Protein Language Model Training, Sharing and Collaboration
• CryoDRGN-AI: Neural ab initio reconstruction of challenging cryo-EM and cryo-ET datasets
• The future of integrated structural biology
• Path Gradients after Flow Matching
• InvDesFlow-AL: active learning-based workflow for inverse design of functional materials
• PSBench: a large-scale benchmark for estimating the accuracy of protein complex structural models
• Protein FID: Improved Evaluation of Protein Structure Generative Models
• Bridging Large Language Models and Single-Cell Transcriptomics in Dissecting Selective Motor Neuron Vulnerability
• Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule
• A Case Cluster of Aseptic Meningitis Associated With a Newly Identified Recombinant Echovirus 6/Coxsackievirus B1 Enterovirus
• Multi-Objective-Guided Discrete Flow Matching for Controllable Biological Sequence Design
• Foam-Agent: Towards Automated Intelligent CFD Workflows
• Bioengineering of long-chain polyunsaturated fatty acids in oilseed crops
• PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking
• The fitness landscape of overlapping genes
• Latent-Y: A Lab-Validated Autonomous Agent for De Novo Drug Design
• Scoring-Assisted Generative Exploration for Proteins (SAGE-Prot): A Framework for Multi-Objective Protein Optimization via Iterative Sequence Generation and Evaluation
• Hidden proteins encoded by non-canonical open reading frames: A review
• Vision Transformers and Graph Neural Networks for Charged Particle Tracking in the ATLAS Muon Spectrometer
• A Wireless World Model for AI-Native 6G Networks
• Rethinking Benchmarks and Models for Enzyme Specificity Prediction
• ZeroFold: Protein-RNA Binding Affinity Predictions from Pre-Structural Embeddings
• Learning Hamiltonian Flow Maps: Mean Flow Consistency for Large-Timestep Molecular Dynamics
• Expanding Protein Structure Prediction into Conformational State Space
• Towards a new paradigm of scientific discovery with socialized artificial intelligence
• G2P Explorer: A Native iOS Framework for Residue-Level Genomics to Proteomics Visualization and Structural Variant Interpretation
• UMA-Inverse: Ligand-Conditioned Protein Inverse Folding with a Distogram-Supervised Dense Pair Encoder
• Folding, Reasoning, and Scaling with Open-source Drug Discovery Engine
• Atomic Trajectory Modeling with State Space Models for Biomolecular Dynamics
• Structure-Regularized Interpretable TCR-Epitope Prediction
• Oligosaccharide oxidase for the enzymatic synthesis of glucosaminic acids
• scpFormer: A Foundation Model for Unified Representation and Integration of the Single-Cell Proteomics
• Adaptive Protein Tokenization
• De novo design of protein binders targeting the human sweet taste receptor as potential sweet proteins
• Astrobiology in the Time of Artificial Intelligence
• DPP8/9 processing of human AK2 unmasks an IAP binding motif
• HIDDENdb: Co-dependency database reveals a plethora of genetic and protein interactions
• A Systematic Evaluation of Co-folding Model Representations for Small-Molecule Learning
• The resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to crops
• AlloGen: Conformation-Selective Binder Generation with Differential State Scoring
• CryoNet.Refine: A One-step Diffusion Model for Rapid Refinement of Structural Models with Cryo-EM Density Map Restraints
• RIDER: 3D RNA Inverse Design with Reinforcement Learning-Guided Diffusion
• GPU Forecasters: Language Models as Selective Surrogates for Kernel Runtime Optimization
• Site4Drug: Predicting Drug-Binding Target Sites with an AI Agent
• Demystifying Multimodal Biomolecular Co-design With Intrinsic Geodesic Coupling
• Peptide Structure Prediction Using Counter-Diabatic Quantum Approximate Optimization Algorithm (CD-QAOA)
• On the Relationship Between Activation Outliers and Feature Death in Sparse Autoencoders
• AMix-2: Establishing Protein as a Native Modality in Large Language Models
• Hermes: Large DEL Datasets Train Generalizable Protein-Ligand Binding Prediction Models
• SurfDesign: Effective Protein Design on Molecular Surfaces
• Atom-level Protein Representation Learning Improves Protein Structure Prediction
• High-yield production and functional analysis of novel rhizobial-type glutaminase-free l-asparaginase from Paenibacillus thiaminolyticus
• AI and omics technologies in biobanking: Applications and challenges for public health
• Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design
• Frequency-Space Mechanics: A Sequence and Coordinate-Free Representation for Protein Function Prediction
• Protein Circuit Tracing via Cross-layer Transcoders
• ProtDBench: A Unified Benchmark of Protein Binder Design and Evaluation
• Accurate, Interdisciplinary and Transparent Structure-property Understanding with Deep Native Structural Reasoning
• CrystalBoltz: End-to-End Protein Structure Determination via Experiment-Guided Diffusion for X-Ray Crystallography
• Perspective on Bias in Biomedical AI: Preventing Downstream Healthcare Disparities
• On the Reliability of AI Methods in Drug Discovery: Evaluation of Boltz-2 for Structure and Binding Affinity Prediction
• Inference-time optimization for experiment-grounded protein ensemble generation
• Protein Graph Neural Networks for Heterogeneous Cryo-EM Reconstruction
• AtomMOF: All-Atom Flow Matching for MOF-Adsorbate Structure Prediction
• EvoMaster: A Foundational Evolving Agent Framework for Agentic Science at Scale
• A Unified Predictive and Generative Solution for Liquid Electrolyte Formulation
• Action-Minimization Meets Generative Modeling: Efficient Transition Path Sampling with the Onsager-Machlup Functional
• Polyformer: a generative framework for thermodynamic modeling of polymeric molecules
• ViraHinter: a dual-modal artificial intelligence framework for predicting virus-host interactions
• MuCO: Generative Peptide Cyclization Empowered by Multi-stage Conformation Optimization
• AI Developments for T and B Cell Receptor Modeling and Therapeutic Design
• DiverseDiT++: Quantifying, Analyzing, and Promoting Representation Diversity in Diffusion Transformers
• Fold-switching proteins push the boundaries of conformational ensemble prediction
• SeedProteo: Accurate De Novo All-Atom Design of Protein Binders
• polyGen: A Learning Framework for Atomic-level Polymer Structure Generation
• P1642-1, a novel pancreatic polypeptide analogue, ameliorates cognitive impairment in 5 ×FAD mice and is associated with enhanced PINK1/Parkin-related mitophagy
• A guide to building the matrisome interactome: from computational predictions to experimental validation
• A Blind Spot in Alignment: Quantifying Biosecurity Risks in Large Language Models
• A Folding-Docking-Affinity framework for protein-ligand binding affinity prediction
• RiboSphere: Learning Unified and Efficient Representations of RNA Structures
• Accurate and generalizable protein-ligand binding affinity prediction with geometric deep learning
• Cell cycle follows “pause and play” mechanism in environment stress recovery in diverse plant species
• Clifford Group Equivariant Diffusion Models for 3D Molecular Generation
• Quantum Doubly Stochastic Transformers
• Heterogeneous networks in drug-target interaction prediction
• Language Models for Materials Discovery and Sustainability: Progress, Challenges, and Opportunities
• EIoT: Embodied Intelligence of Things
• Artificial intelligence in drug discovery — what it is, where we stand and the path forward
• An All-Atom Generative Model for Designing Protein Complexes
• Topologically Directed Simulations Reveal the Impact of Geometric Constraints on Knotted Proteins
• Probing the effects of broken symmetries in machine learning
• Alzheimer’s Disease Prevention by Snake Venoms
• AI-guided Antibiotic Discovery Pipeline from Target Selection to Compound Identification
• Elucidating the Design Space of Multimodal Protein Language Models
• FLOWR: Flow Matching for Structure-Aware De Novo, Interaction- and Fragment-Based Ligand Generation
• Valorization of Ficus carica Pruning Residues as Selective Botanical Insecticides: Optimized Furanocoumarin Extraction, Efficacy Against Neotropical Stink Bugs, and Mechanistic Insights via Molecular Docking
• Neural Encoding and Decoding at Scale
• PolyConf: Unlocking Polymer Conformation Generation through Hierarchical Generative Models
• Compositional Flows for 3D Molecule and Synthesis Pathway Co-design
• Programmable antisense oligomers for phage functional genomics
• 14-3-3 λ suppresses ethylene-mediated root growth inhibition through EIN3/EIL1 in Aratbidopsis
• A lettuce receptor-like kinase recognizes the highly conserved heptapeptide motif within microbial Nep1-like proteins

Discussions

• Accurate structure prediction of biomolecular interactions with AlphaFold 3 doi.org/10.1038/s415... But: no code, no binary, and what appears to be a limited webserver [bsky, 3 points, 2 comments]

Related

• AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?
• Structural Biology of RNA and Protein‐RNA Complexes after AlphaFold3
• High-accuracy protein complex structure modeling based on sequence-derived structure complementarity
• Protein complex prediction with AlphaFold-Multimer
• From Prediction to Simulation: AlphaFold 3 as a Differentiable Framework for Structural Biology