Comparative Protein Modelling by Satisfaction of Spatial Restraints

1993/12/01 by Andrej Šali, Tom L. Blundell · 65 citations
Biochemistry, Genetics and Molecular Biology · Materials Science · #Protein Structure and Dynamics #Glycosylation and Glycoproteins Research #Enzyme Structure and Function

paper · doi:10.1006/jmbi.1993.1626

Cited by

• Ligand-supported Homology Modelling of Protein Binding-sites using Knowledge-based Potentials
• Thermodynamic Destabilization and Structural Adaptability of 2′-Alkoxy/Fluoro-<i>N</i>³-Methyl Pyrimidine Nucleotides in siRNA Enhance RNA Interference Activity
• Kinetic characterization, structure modelling studies and crystallization of <i>Trypanosoma brucei</i> enolase
• Full-Length Molecular Models of Brain-Derived α-Synuclein Fibrils Reveal a Fuzzy-Coat-Mediated Mechanism for Selective Peptide Binding
• The reactions catalysed by the mitochondrial uncoupling proteins UCP2 and UCP3
• Plant membrane assays with cytokinin receptors underpin the unique role of free cytokinin bases as biologically active ligands
• Model of interaction of the IL‐1 receptor accessory protein IL‐1RAcP with the IL‐1β/IL‐1R_I complex
• Noncompetitive Inhibition of 5-HT3 Receptors by Citral, Linalool, and Eucalyptol Revealed by Nonlinear Mixed-Effects Modeling
• Selective Cannabinoid 2 Receptor Stimulation Reduces Tubular Epithelial Cell Damage after Renal Ischemia-Reperfusion Injury
• Determinants of Zinc Potentiation on the α4 Subunit of Neuronal Nicotinic Receptors
• The ICl,swell inhibitor DCPIB blocks Kir channels that possess weak affinity for PIP2
• Simulation-based survey of TMEM16 family reveals that robust lipid scrambling requires an open groove
• Distinct Valence States of the [4Fe4S] Cluster Revealed in the Hydrogenase <i>Cr</i> HydA1
• Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming
• Advancements in Nanobody Epitope Prediction: A Comparative Study of AlphaFold2Multimer vs AlphaFold3
• A Wnt-induced conformational phospho-switch in DVL3 controls interaction with Frizzled receptors and Wnt/β-catenin signaling
• Conformational Profile of Galactose‐α‐1,3‐Galactose (α‐Gal) and Structural Basis of Its Immunological Response
• Continuum architecture dynamics of vesicle tethering in exocytosis
• Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference
• QFoldAgent: An Autonomous Quantum Optimization Multi-Agent System for Protein Structure Prediction
• Realistic Transition Paths for Large Biomolecular Systems: A Langevin Bridge Approach
• A structural biology community assessment of AlphaFold2 applications
• Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12
• Petascale Homology Search for Structure Prediction
• An Automatable Analytical Algorithm for Structure-Based Protein\n Functional Annotation via Detection of Specific Ligand 3D Binding Sites:\n Application to ATP (ser/thr Protein Kinases) and GTP (Small Ras-type\n G-Proteins) Binding Sites
• R-loop control and mitochondrial genome stability require the 5′-3′ exonuclease/flap endonuclease OEX1
• Systematic discovery of pro- and anti-HIV host factors in primary human CD4+ T cells
• The unique mutation in <i>ace‐1</i> giving high insecticide resistance is easily detectable in mosquito vectors
• Evolutionary History and Functional Divergence of Hydroxycarboxylic Acid Receptors in Primates
• Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8
• Physics‐based protein structure refinement in the era of artificial intelligence
• Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation‐induced damage
• Evolutionary remodeling of the FXR binding pocket drove functional divergence and ligand discrimination
• Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets
• Scoring function for automated assessment of protein structure template quality
• Aminoquinoline Fluorescent Labels Obstruct Efficient Removal of <i>N</i>-Glycan Core α(1–6) Fucose by Bovine Kidney α-<scp>l</scp>-Fucosidase (BKF)
• Early neurological symptoms and epilepsy outcomes in individuals with the recurrent <scp> <i>GABRG2</i> </scp> p.( <scp>Ala106Thr</scp> ) gain‐of‐function variant: Structural and phenotypic insights
• Single-residue engineering of lambda (λ) antibody light chains reduces conformational flexibility and enhances thermal stability
• DNA induces non-canonical dimerization of the farnesoid X receptor
• Cellular Responses in the Pigeonpea Wild Relative <i>Cajanus platycarpus</i> to <i>Helicoverpa armigera</i> Herbivory: The Role of Methionine Sulfoxide Reductase B1 ( <i>CpMSRB1</i> ) in Enhanced Defense
• A human monoclonal antibody neutralizes SARS-CoV-2 Omicron variants by targeting the upstream region of spike protein HR2 motif
• Structural modeling and functional characterization of a novel gain-of-function TLR8 variant causing severe inflammatory syndrome
• <i>In situ</i> molecular organization and heterogeneity of the <i>Legionella</i> Dot/Icm <scp>T4SS</scp>
• Structural genomics: A pipeline for providing structures for the biologist
• Statistical potential for assessment and prediction of protein structures
• Siglec-7 mediates nonapoptotic cell death independently of its immunoreceptor tyrosine-based inhibitory motifs in monocytic cell line U937
• Influence of ionic liquids on enzymatic asymmetric carboligations
• An atomic look at the interface of GHSR and its partners
• Evolution of the SARS-CoV-2 spike protein in utilizing host transmembrane serine proteases
• Evolutionary and Functional Analysis of Caspase-8 and ASC Interactions to Drive Lytic Cell Death, PANoptosis
• Unusual catalytic strategy by non-heme Fe( <scp>ii</scp> )/2-oxoglutarate-dependent aspartyl hydroxylase AspH
• Bayesian Nonparametric Analysis of Residence Times for Protein–Lipid Interactions in Molecular Dynamics Simulations
• Citrullination at the N‐terminal region of <scp>MDM2</scp> by the <scp>PADI4</scp> enzyme
• <scp>PEG–mCherry</scp> interactions beyond classical macromolecular crowding
• Molecular dynamics simulations: advances and applications
• NNDock2: A neural network-based scoring function for ranking protein–protein docking models
• Dual-ActionTetrapeptide Analogue of PsychrophilicFungal Origin: Potent Inhibitor of Human Nicotinic Acetylcholine Receptorswith Antinociceptive and Muscle-Relaxant Activity
• Structural and catalytic consequences of active-site <i>vs.</i> distal mutations in human dehalogenase: insights from molecular dynamics simulations
• QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts
• Highly accurate protein structure prediction with AlphaFold
• Computational modeling of biological nanopores
• Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation
• Autism with Seizures and Intellectual Disability: Possible Causative Role of Gain-of-function of the Inwardly-Rectifying K+ Channel Kir4.1
• A triple-action PROTAC for wild-type p53 cancer therapy
• Sulfated glycosaminoglycans inhibit LCMV entry and modulate antiviral immunity and pathology