CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

An algorithm for the machine calculation of complex Fourier series

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A general method applicable to the search for similarities in the amino acid sequence of two proteins

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‘GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers’

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CHARMM‐GUI: A web‐based graphical user interface for CHARMM

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Cp2k: An electronic structure and molecular dynamics software package-quickstep: Efficient and accurate electronic structure calculations

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Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery

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The General Utility Lattice Program ( GULP )

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Identification of RIP1 kinase as a specific cellular target of necrostatins

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The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

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A Switch Between Two-, Three-, and Four-stranded Coiled Coils in GCN4 Leucine Zipper Mutants

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ZDOCK: An initial‐stage protein‐docking algorithm

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A new approach to protein fold recognition

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Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding

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Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

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Constructing high‐dimensional neural network potentials: A tutorial review

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Neural network potential-energy surfaces in chemistry: a tool for large-scale simulations

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Two Binding Orientations for Peptides to the Src SH3 Domain: Development of a General Model for SH3-Ligand Interactions

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Calculation of absolute protein–ligand binding free energy from computer simulations

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Absolute Binding Free Energies: A Quantitative Approach for Their Calculation

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Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF)

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F ROM F OLDING T HEORIES TO F OLDING P ROTEINS: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding

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Reaction coordinates of biomolecular isomerization

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Multiple diverse ligands binding at a single protein site: A matter of pre‐existing populations

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Automatic Method for Identifying Reaction Coordinates in Complex Systems

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Overcoming mutation-based resistance to antiandrogens with rational drug design

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Zinc binding in proteins and solution: A simple but accurate nonbonded representation

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The binding sites for cocaine and dopamine in the dopamine transporter overlap

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Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

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Solution structure of the N-terminal zinc binding domain of HIV-1 integrase

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Binding MOAD (Mother Of All Databases)

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Activation pathway of Src kinase reveals intermediate states as targets for drug design

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Solution Structure of the DNA Binding Domain of HIV-1 Integrase

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Progress in Modeling of Protein Structures and Interactions.

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A Post-Synaptic Scaffold at the Origin of the Animal Kingdom

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A Small-Molecule Inhibitor of BCL6 Kills DLBCL Cells In Vitro and In Vivo

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Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

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Protein elastic network models and the ranges of cooperativity

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Persistent homology analysis of protein structure, flexibility, and folding

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Molecular driving forces determining potassium channel slow inactivation

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Structural basis for hijacking of cellular LxxLL motifs by papillomavirus E6 oncoproteins

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Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations

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A gate in the selectivity filter of potassium channels

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The discovery of potential acetylcholinesterase inhibitors: A combination of pharmacophore modeling, virtual screening, and molecular docking studies

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Prediction of aggregation prone regions of therapeutic proteins

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A physical reference state unifies the structure-derived potential of mean force for protein folding and binding

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Germline KRAS mutations cause aberrant biochemical and physical properties leading to developmental disorders

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Relation between native ensembles and experimental structures of proteins

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Force Generation in Kinesin Hinges on Cover-Neck Bundle Formation

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Mitochondrial-Targeted Plastoquinone Derivatives. Effect on Senescence and Acute Age-Related Pathologies

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Historical contingency and its biophysical basis in glucocorticoid receptor evolution

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Analysis of the migration behaviour of single microtubules in electric fields

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Computational studies of membrane channels

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Conformation of the HIV-1 Gag Protein in Solution

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CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

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Antibody modeling assessment

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Molecular dynamics simulations of tubulin structure and calculations of electrostatic properties of microtubules

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Martinize2 and Vermouth provide a unified framework for molecular topology generation

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The Solution Structure of DNA Duplex-Decamer Containing the (6-4) Photoproduct of Thymidylyl(3'5')Thymidine by NMR and Relaxation Matrix Refinement

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Distinct recognition modes of FXXLF and LXXLL motifs by the androgen receptor

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MutaBind estimates and interprets the effects of sequence variants on protein–protein interactions

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Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol

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Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity

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Solution structure of the ets domain of Fli-1 when bound to DNA

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Multiscale multiphysics and multidomain models—Flexibility and rigidity

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A topological approach for protein classification

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Interactions of Human Melanocortin 4 Receptor with Nonpeptide and Peptide Agonists,

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An overview of the prediction of protein DNA-binding sites

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Coarse graining of short polythylene chains for studying polymer crystallization

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Biomolecular simulation and modelling: status, progress and prospects

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Structural and Functional Impact of Parkinson Disease-Associated Mutations in the E3 Ubiquitin Ligase Parkin: HUMAN MUTATION

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All-Atom Ab Initio Folding of a Diverse Set of Proteins

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Context-Based Identification of Protein-Protein Interfaces and “Hot-Spot” Residues

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High-affinity interaction of the K-Ras4B hypervariable region with the RAS active site

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Structural Features of the αβTCR Mechanotransduction Apparatus That Promote pMHC Discrimination

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Towards a Structure for a TSG-6·Hyaluronan Complex by Modeling and NMR Spectroscopy

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Dimensions of Biological Cellulose Nanocrystals Maximize Fracture Strength

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Interactions of macromolecules with salt ions: An electrostatic theory for the Hofmeister effect

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Integrative structure modeling of macromolecular assemblies from proteomics data

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Correction of the NMR structure of the ETS1/DNA complex

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Design Challenges for Hemoproteins: The Solution Structure of Apocytochrome b5,

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Identification of the dominant photochemical pathways and mechanistic insights to the ultrafast ligand exchange of Fe(CO)5 to Fe(CO)4EtOH

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Antibody H3 structure prediction

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Challenges in the computational design of proteins

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Transitions in microtubule C-termini conformations as a possible dendritic signaling phenomenon

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Seeking structural specificity: direct modulation of pentameric ligand-gated ion channels by alcohols and general anesthetics

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Models of the Structure and Voltage-Gating Mechanism of the Shaker K+ Channel

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Nucleotide modifications and tRNA anticodon–mRNA codon interactions on the ribosome

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E Stereoregular 1,1 and 1,3 Constitutional Units from 1,3-Butadiene in Copolymerizations Catalyzed by a Highly Hindered C2 Symmetric Metallocene

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The catalytic mechanism of fluoroacetate dehalogenase: a computational exploration of biological dehalogenation

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A switch point in the molecular chaperone Hsp90 responding to client interaction

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Molecular basis of Wnt biogenesis, secretion, and Wnt7-specific signaling

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FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules

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Kinesin Has Three Nucleotide-dependent Conformations

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Structural stability of proteins in aqueous and nonpolar environments

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A computational study of Mg2+ dehydration in aqueous solution in the presence of HS− and other monovalent anions – Insights to dolomite formation

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Harnessing fluoroacetate dehalogenase for defluorination of fluorocarboxylic acids: in silico and in vitro approach

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