AmberTools

2023/10/08 by David A. Case, Hasan Metin Aktulga, Kellon Belfon +44 · 55 citations
Biochemistry, Genetics and Molecular Biology · Decision Sciences · #Metabolomics and Mass Spectrometry Studies #Protein Structure and Dynamics #Scientific Computing and Data Management

paper · pdf · doi:10.1021/acs.jcim.3c01153

openalex publication_date 2023/10/08 · openalex created_date 2023/10/10 · openalex updated_date 2026/07/30

Abstract

High Resolution Image Download MS PowerPoint Slide AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.

Citations

• A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
• Development and testing of a general amber force field

Cited by

• Improvement of the density fitting approach for the Gaussian electrostatic model via the use of the discrete Picard condition in Tychonov regularization
• Deciphering the evolutionary origin of the enantioselectivity of short-chain dehydrogenases from plants toward 1-borneol
• Harnessing AlphaFold to reveal hERG channel conformational state secrets
• The mycotoxin Beauvericin is an uncompetitive inhibitor of Cathepsin B
• Aggregation-dependent epitope sequence and modification fingerprints of anti-Aβ antibodies
• Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model
• All-Atom Membrane Builder via Multiscale Simulation
• Effect of histidine on the antimicrobial peptide maculatin 1.1 solution-state NMR and molecular dynamics simulation structures at different protonation states
• ¹⁹ F NMR as a tool to probe drug binding and structural dynamics in ferritin-based nanocarriers
• Electrostatic embedding machine learning for ground and excited state molecular dynamics of solvated molecules
• Large-scale energy decomposition for the analysis of protein stability
• Investigating the structural basis of surfactant protein D oligomerization: The crucial role of Cys15‐Cys15/Cys20‐Cys20 disulfide bond linkage
• Evolutionary remodeling of the FXR binding pocket drove functional divergence and ligand discrimination
• Uncovering the flexibility of CDR loops in antibodies and TCRs through large-scale molecular dynamics
• Cryo-EM reveals molecular mechanisms underlying the inhibitory effect of netrin-4 on laminin matrix formation
• dynsight: an Open Python Platform for Simulation and Experimental Trajectory Data Analysis
• Switching on Supramolecular DNA Junction Binding Using a Human Enzyme
• Uncertainty-Aware Multi-Objective Reinforcement Learning-Guided Diffusion Models for 3D De Novo Molecular Design
• Transient dynamics of flavonoid metabolons tune chalcone synthase specificity
• Transferable Generative Models Bridge Femtosecond to Nanosecond Time-Step Molecular Dynamics
• Simulating enzyme catalysis with electrostatically embedded machine learning potentials
• Designing mimosine-containing peptides as efficient metal chelators: Insights from molecular dynamics and quantum calculations
• When does molecular dynamics improve RNA models? Insights from CASP15 and practical guidelines
• Antagonist Binding Actively Disrupts Interleukin-1 Receptor Dynamics to Block Co-receptor Recruitment
• Identification of a novel TLR7 gain-of-function variant that underlies systemic lupus erythematosus
• Identification of the trail-following pheromone receptor in termites
• Predicting non-covalent interactions between antioxidants in biological membranes through molecular dynamics
• A computational pipeline for predicting distal hotspots in an artificial enzyme
• RNA codon expansion via programmable pseudouridine editing and decoding
• Machine learning-driven classification of bioactive peptides and their molecular basis for sour taste perception
• STEPs-SOL, a Peptoid Force Field Parameterization to Include Solvent Effects
• Development of an Optimized Parameter Set for Monovalent Ions in the Reference Interaction Site Model of Solvation
• Intercalation Favors DNA Covalent Photobinding in Photoresponsive Dual PDT/PCT Bimetallic Assemblies
• Adaptive evolution of electron transfer pathways in <i>Thermoanaerobacterium saccharolyticum</i>
• Structural modeling and functional characterization of a novel gain-of-function TLR8 variant causing severe inflammatory syndrome
• Genetic control of morphological transitions in a coacervating protein template
• Multiscale computational insights into 5-fluorouracil delivery <i>via</i> zeolite imidazole frameworks (ZIFs)
• An artificial intelligence accelerated virtual screening platform for drug discovery
• Evolution of the SARS-CoV-2 spike protein in utilizing host transmembrane serine proteases
• Streamlining Coding Assignments and Grading on the Cloud: A Preconfigured JupyterHub Image for Chemistry Education
• Resveratrol and Its Metabolite as Potential Allosteric Regulators of Monoamine Oxidase A Activity in the Brain and Liver Under Chronic Predator Stress
• Glycoproteomic and Single-Protein Glycomic Analyses Reveal Zwitterionic N-Glycans on Natural and Recombinant Proteins Derived From Insect Cells
• A system of paired polyether epoxide hydrolases enables a mouldable enzyme for consecutive ring cyclization cascades
• Interactions of elongated dinuclear metallo-cylinders with DNA three-way and four-way junctions
• The Protein Force Field Plays a Crucial Role in Obtaining Accurate Macromolecular Ensembles of IDPs
• Sesame: Opening the door to protein pockets
• Equipartition and the temperature of maximum density of TIP4/2005 water
• Performance of universal machine-learned potentials with explicit long-range interactions in biomolecular simulations
• Sulfated glycosaminoglycans inhibit LCMV entry and modulate antiviral immunity and pathology
• Efficacy of binders on sequestering per- and polyfluoroalkyl substances under in vitro ruminal conditions
• Investigating the Role of pH and Counterions in the Intrinsic Fluorescence of Solid-State L-Lysine
• <i>n</i> P-Collabs: Investigating Counterion-Mediated Bridges in the Multiply Phosphorylated Tau-R2 Repeat
• Promiscuous binding peptides—Computational screening reveals higher-affinity peptides for gold binding beyond phage display selections
• Wrapping it up: structural basis of ADAMTS-13 global latency
• Rational design of gold nanoparticles functionalized with aptamers for improved West Nile virus detection

Related

• CHARMM‐GUI: A web‐based graphical user interface for CHARMM
• SEAMM: A Simulation Environment for Atomistic and Molecular Modeling
• Molcontroller: a VMD Graphical User Interface for Manipulating Molecules
• Development &amp; Implementation of a PyMOL 'putty' Representation
• CHARMM‐GUI 10 years for biomolecular modeling and simulation