On the public citation graph
Free Energy Simulations Come of Age: Protein−Ligand Recognition
0 signed · 433 inferred · view as graph
Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.
Is this your work? Sign in with ORCID and put your name on the
claims that are yours.
Reference health. See whether every reference in this work resolves to a
known work and none has been retracted — and get a dated CiteStamped
badge you can embed.
What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199908)20:11<1091::aid-jcc1>3.0.co;2-3openalex-snapshot
Multiple-site ligand binding to flexible macromolecules: Separation of global and local conformational change and an iterative mobile clustering approach
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19980901)32:4<399::aid-prot1>3.0.co;2-copenalex-snapshot
Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19981001)33:1<39::aid-prot4>3.0.co;2-gopenalex-snapshot
Calculation of HyHel10-lysozyme binding free energy changes: Effect of ten point mutations
inferredcites →https://doi.org/10.1002/pro.5560030206openalex-snapshot
Do salt bridges stabilize proteins? A continuum electrostatic analysis
inferredcites →https://doi.org/10.1002/pro.5560060617openalex-snapshot
On the calculation of binding free energies using continuum methods: Application to MHC class I protein‐peptide interactions
inferredcites →https://doi.org/10.1002/prot.340160303openalex-snapshot
Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches
inferredcites →https://doi.org/10.1002/prot.340200105openalex-snapshot
Free energy simulations: The meaning of the individual contributions from a component analysis
inferredcites →https://doi.org/10.1006/jmbi.1995.0656openalex-snapshot
The Meaning of Component Analysis: Decomposition of the Free Energy in Terms of Specific Interactions
inferredcites →https://doi.org/10.1006/jmbi.1997.1470openalex-snapshot
Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations 1 1A. R. Fersht
inferredcites →https://doi.org/10.1006/jmbi.1999.3319openalex-snapshot
Investigating the binding specificity of U1A-RNA by computational mutagenesis
inferredcites →https://doi.org/10.1006/jmbi.2000.4285openalex-snapshot
Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase11Edited by A. R. Fersht
inferredcites →https://doi.org/10.1016/0009-2614(87)80646-2openalex-snapshot
Calculation of free energy surfaces using the methods of thermodynamic perturbation theory
inferredcites →https://doi.org/10.1016/0009-2614(94)00397-1openalex-snapshot
Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations
inferredcites →https://doi.org/10.1016/s0006-3495(91)82311-6openalex-snapshot
Ion transport in a model gramicidin channel. Structure and thermodynamics
inferredcites →https://doi.org/10.1016/s0006-3495(97)78756-3openalex-snapshot
The statistical-thermodynamic basis for computation of binding affinities: a critical review
inferredcites →https://doi.org/10.1016/s0009-2614(89)87314-2openalex-snapshot
Constrained reaction coordinate dynamics for the simulation of rare events
inferredcites →https://doi.org/10.1016/s0959-440x(00)00197-4openalex-snapshot
Macromolecular electrostatics: continuum models and their growing pains
inferredcites →https://doi.org/10.1016/s0959-440x(98)80046-8openalex-snapshot
Theory of biomolecular recognition
inferredcites →https://doi.org/10.1016/s1359-0278(96)00056-9openalex-snapshot
Double-mutant cycles: a powerful tool for analyzing protein structure and function
inferredcites →https://doi.org/10.1021/ar000079copenalex-snapshot
NMR Relaxation Studies of the Role of Conformational Entropy in Protein Stability and Ligand Binding
inferredcites →https://doi.org/10.1021/ar950181nopenalex-snapshot
Why Is It So Difficult To Simulate Entropies, Free Energies, and Their Differences?
inferredcites →https://doi.org/10.1021/bi000704lopenalex-snapshot
Estimation of the Hydrophobic Effect in an Antigen−Antibody Protein−Protein Interface ,
inferredcites →https://doi.org/10.1021/bi00151a037openalex-snapshot
Thermodynamics of protein-peptide interactions in the ribonuclease-S system studied by molecular dynamics and free energy calculations
inferredcites →https://doi.org/10.1021/bi00227a009openalex-snapshot
Simulation analysis of the stability mutant R96H of T4 lysozyme
inferredcites →https://doi.org/10.1021/bi00227a010openalex-snapshot
Effects of inhibitors of N-linked oligosaccharide processing on the secretion, stability, and activity of lecithin:cholesterol acyltransferase
inferredcites →https://doi.org/10.1021/bi00374a006openalex-snapshot
Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process
inferredcites →https://doi.org/10.1021/bi00374a007openalex-snapshot
Domain organization of chicken gizzard myosin light chain kinase deduced from a cloned cDNA
inferredcites →https://doi.org/10.1021/bk-1981-0173.ch012openalex-snapshot
Computer Simulation of Biomolecular Systems
inferredcites →https://doi.org/10.1021/cr00023a004openalex-snapshot
Free energy calculations: Applications to chemical and biochemical phenomena
inferredcites →https://doi.org/10.1021/ja00273a049openalex-snapshot
Phosphorothioite method. 1. A new type of internucleotidic bond formation involving simultaneous oxidation process by use of deoxyoligonucleoside phosphorothioites as new key intermediates for deoxyoligonucleotide synthesis
inferredcites →https://doi.org/10.1021/ja010716+openalex-snapshot
Dielectric Relaxation in an Enzyme Active Site: Molecular Dynamics Simulations Interpreted with a Macroscopic Continuum Model
inferredcites →https://doi.org/10.1021/ja963568+openalex-snapshot
Inclusion of Loss of Translational and Rotational Freedom in Theoretical Estimates of Free Energies of Binding. Application to a Complex of Benzene and Mutant T4 Lysozyme
inferredcites →https://doi.org/10.1021/ja984414sopenalex-snapshot
Hydrophobic Force Field as a Molecular Alternative to Surface-Area Models
inferredcites →https://doi.org/10.1021/ja990935jopenalex-snapshot
Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies
inferredcites →https://doi.org/10.1021/jm000443dopenalex-snapshot
Computational Analysis of PKA−Balanol Interactions
inferredcites →https://doi.org/10.1021/jm001045dopenalex-snapshot
Simulations of the Estrogen Receptor Ligand-Binding Domain: Affinity of Natural Ligands and Xenoestrogens
inferredcites →https://doi.org/10.1021/jp0014317openalex-snapshot
Electrostatic Free Energy Calculations for Macromolecules: A Hybrid Molecular Dynamics/Continuum Electrostatics Approach
inferredcites →https://doi.org/10.1021/jp0017341openalex-snapshot
Calculation of the Potential of Mean Force for the Binding of Glucose to Benzene in Aqueous Solution
inferredcites →https://doi.org/10.1021/jp001760zopenalex-snapshot
Free-Energy Perturbation Calculations of DNA Destabilization by Base Substitutions: The Effect of Neutral Guanine·Thymine, Adenine·Cytosine and Adenine·Difluorotoluene Mismatches
inferredcites →https://doi.org/10.1021/jp962478oopenalex-snapshot
The Reorganization Energy of Cytochrome c Revisited
inferredcites →https://doi.org/10.1021/jp9711499openalex-snapshot
Continuum Treatment of Long-Range Interactions in Free Energy Calculations. Application to Protein−Ligand Binding.
inferredcites →https://doi.org/10.1021/jp991354jopenalex-snapshot
A Poisson−Boltzmann Study of Charge Insertion in an Enzyme Active Site: The Effect of Dielectric Relaxation
inferredcites →https://doi.org/10.1038/314235a0openalex-snapshot
Hydrogen bonding and biological specificity analysed by protein engineering
inferredcites →https://doi.org/10.1038/314238a0openalex-snapshot
New quasars with z = 3.4 and 3.7 and the surface density of very high redshift quasars
inferredcites →https://doi.org/10.1038/35009114openalex-snapshot
Ion permeation mechanism of the potassium channel
inferredcites →https://doi.org/10.1038/35009119openalex-snapshot
CD1c-mediated T-cell recognition of isoprenoid glycolipids in Mycobacterium tuberculosis infection
inferredcites →https://doi.org/10.1038/35099587openalex-snapshot
Uracil-DNA glycosylase acts by substrate autocatalysis
inferredcites →https://doi.org/10.1051/jcp/1991882419openalex-snapshot
On the treatment of electrostatic interactions in biomolecular simulation
inferredcites →https://doi.org/10.1063/1.471472openalex-snapshot
Free energy simulations: Correcting for electrostatic cutoffs by use of the Poisson equation
inferredcites →https://doi.org/10.1063/1.472358openalex-snapshot
The Jacobian factor in free energy simulations
inferredcites →https://doi.org/10.1063/1.480139openalex-snapshot
Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling
inferredcites →https://doi.org/10.1073/pnas.071034098openalex-snapshot
Free energy reconstruction from nonequilibrium single-molecule pulling experiments
inferredcites →https://doi.org/10.1073/pnas.181342398openalex-snapshot
Electrostatics of nanosystems: Application to microtubules and the ribosome
inferredcites →https://doi.org/10.1073/pnas.92.4.1082openalex-snapshot
Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution.
inferredcites →https://doi.org/10.1073/pnas.96.25.14330openalex-snapshot
Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7
inferredcites →https://doi.org/10.1080/00268979300102371openalex-snapshot
Free energy of particle insertion
inferredcites →https://doi.org/10.1107/s0021889891004387openalex-snapshot
EPITAX: a computer-assisted graphical representation of the bicrystallography of general interfaces
inferredcites →https://doi.org/10.1107/s0021889891004399openalex-snapshot
MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
inferredcites →https://doi.org/10.1107/s0907444994006396openalex-snapshot
Raster3D Version 2.0. A program for photorealistic molecular graphics
inferredcites →https://doi.org/10.1110/ps.8.1.50openalex-snapshot
Protein‐protein recognition: An experimental and computational study of the R89K mutation in Raf and its effect on Ras binding
inferredcites →https://doi.org/10.1110/ps.8.5.958openalex-snapshot
Energetic analysis of an antigen/antibody interface: Alanine scanning mutagenesis and double mutant cycles on the hyhel‐10/lysozyme interaction
inferredcites →https://doi.org/10.1110/ps.8.7.1381openalex-snapshot
Electrostatic interactions in the GCN4 leucine zipper: Substantial contributions arise from intramolecular interactions enhanced on binding
inferredcites →https://doi.org/10.1126/science.2471266openalex-snapshot
Brefeldin A Specifically Inhibits Presentation of Protein Antigens to Cytotoxic T Lymphocytes
inferredcites →https://doi.org/10.1126/science.7618103openalex-snapshot
First-Principles Calculation of the Folding Free Energy of a Three-Helix Bundle Protein
inferredcites →https://doi.org/10.1126/science.7761829openalex-snapshot
Classical Electrostatics in Biology and Chemistry
inferredcites →https://doi.org/10.1146/annurev.biophys.28.1.155openalex-snapshot
MOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES: Long-Range Electrostatic Effects
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.2139/ssrn.4681807openalex-extracted
Optimized Parallelization of Boundary Integral Poisson-Boltzmann Solvers
inferred← citeshttps://doi.org/10.1002/9781119138945.ch14openalex-snapshot
Theoretical Modeling and Simulation of IPNs
inferred← citeshttps://doi.org/10.1002/9783527645947.ch11openalex-snapshot
Free Energy Calculations in Drug Lead Optimization
inferred← citeshttps://doi.org/10.1002/bip.10266openalex-snapshot
Molecular dynamics of biological macromolecules: A brief history and perspective
inferred← citeshttps://doi.org/10.1002/cbic.200500364openalex-snapshot
Free‐Energy Simulations and Experiments Reveal Long‐Range Electrostatic Interactions and Substrate‐Assisted Specificity in an Aminoacyl‐tRNA Synthetase
inferred← citeshttps://doi.org/10.1002/cbic.200600535openalex-snapshot
Protonation Patterns in Tetracycline:Tet Repressor Recognition: Simulations and Experiments
inferred← citeshttps://doi.org/10.1002/cbic.70565openalex-snapshot
Toward Ideal Proximity‐Driven Reactions in Chemical Biology
inferred← citeshttps://doi.org/10.1002/chem.200304847openalex-snapshot
(9Z)‐ and (11Z)‐8‐Methylretinals for Artificial Visual Pigment Studies: Stereoselective Synthesis, Structure, and Binding Models
inferred← citeshttps://doi.org/10.1002/chem.200700040openalex-snapshot
A Quantum Mechanics/Molecular Mechanics Study of the Protein–Ligand Interaction for Inhibitors of HIV‐1 Integrase
inferred← citeshttps://doi.org/10.1002/chin.200237290openalex-snapshot
ChemInform Abstract: Free Energy Simulations Come of Age: Protein—Ligand Recognition
inferred← citeshttps://doi.org/10.1002/cmdc.201600220openalex-snapshot
Discovery of HIV Type 1 Aspartic Protease Hit Compounds through Combined Computational Approaches
inferred← citeshttps://doi.org/10.1002/cphc.200700288openalex-snapshot
In Silico Engineering of Tailored Ink‐Binding Ability at Molecular Printboards
inferred← citeshttps://doi.org/10.1002/ijch.201400009openalex-snapshot
Molecular Dynamics Simulations of Bromodomains Reveal Binding‐Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl‐Lysine
inferred← citeshttps://doi.org/10.1002/jcc.20274openalex-snapshot
Nonuniform charge scaling (NUCS): A practical approximation of solvent electrostatic screening in proteins
inferred← citeshttps://doi.org/10.1002/jcc.20580openalex-snapshot
Role of binding entropy in the refinement of protein–ligand docking predictions: Analysis based on the use of 11 scoring functions
inferred← citeshttps://doi.org/10.1002/jcc.20643openalex-snapshot
Polarizable model potential function for nucleic acid bases
inferred← citeshttps://doi.org/10.1002/jcc.21040openalex-snapshot
Molecular mechanics models for tetracycline analogs
inferred← citeshttps://doi.org/10.1002/jcc.21255openalex-snapshot
Unorthodox uses of Bennett's acceptance ratio method
inferred← citeshttps://doi.org/10.1002/jcc.21274openalex-snapshot
Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity
inferred← citeshttps://doi.org/10.1002/jcc.21287openalex-snapshot
CHARMM: The biomolecular simulation program
inferred← citeshttps://doi.org/10.1002/jcc.21366openalex-snapshot
How to obtain statistically converged MM/GBSA results
inferred← citeshttps://doi.org/10.1002/jcc.21442openalex-snapshot
A molecular mechanics model for imatinib and imatinib:kinase binding
inferred← citeshttps://doi.org/10.1002/jcc.21791openalex-snapshot
Minimum MD simulation length required to achieve reliable results in free energy perturbation calculations: Case study of relative binding free energies of fructose‐1,6‐bisphosphatase inhibitors
inferred← citeshttps://doi.org/10.1002/jcc.21829openalex-snapshot
Avoiding the van der Waals endpoint problem using serial atomic insertion
inferred← citeshttps://doi.org/10.1002/jcc.21859openalex-snapshot
Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM–GBSA calculation
inferred← citeshttps://doi.org/10.1002/jcc.22879openalex-snapshot
Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin–DNA duplex complexes in aqueous solution
inferred← citeshttps://doi.org/10.1002/jcc.23418openalex-snapshot
Computational protein design: The proteus software and selected applications
inferred← citeshttps://doi.org/10.1002/jcc.23490openalex-snapshot
Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation
inferred← citeshttps://doi.org/10.1002/jcc.24230openalex-snapshot
Protein:Ligand binding free energies: A stringent test for computational protein design
inferred← citeshttps://doi.org/10.1002/jcc.25345openalex-snapshot
Combining the polarizable Drude force field with a continuum electrostatic Poisson–Boltzmann implicit solvation model
inferred← citeshttps://doi.org/10.1002/jcc.26221openalex-snapshot
Alchemical free energy calculations via metadynamics: Application to the theophylline‐RNA aptamer complex
inferred← citeshttps://doi.org/10.1002/jcc.27081openalex-snapshot
Solvation free energy arithmetic for small organic molecules
inferred← citeshttps://doi.org/10.1002/jmr.980openalex-snapshot
Alchemical free energy simulations for biological complexes: powerful but temperamental …
inferred← citeshttps://doi.org/10.1002/jmr.996openalex-snapshot
Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl‐transferase P‐site using molecular dynamics simulations with restraining potentials
inferred← citeshttps://doi.org/10.1002/minf.201600052openalex-snapshot
Computational Approaches to the Chemical Equilibrium Constant in Protein‐ligand Binding
inferred← citeshttps://doi.org/10.1002/prot.10368openalex-snapshot
Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair
inferred← citeshttps://doi.org/10.1002/prot.20528openalex-snapshot
Study of the insulin dimerization: Binding free energy calculations and per‐residue free energy decomposition
inferred← citeshttps://doi.org/10.1002/prot.20641openalex-snapshot
Glycogen phosphorylase inhibitors: A free energy perturbation analysis of glucopyranose spirohydantoin analogues
inferred← citeshttps://doi.org/10.1002/prot.21259openalex-snapshot
Protein–protein recognition and interaction hot spots in an antigen–antibody complex: Free energy decomposition identifies “efficient amino acids”
inferred← citeshttps://doi.org/10.1002/prot.21367openalex-snapshot
EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization
inferred← citeshttps://doi.org/10.1002/prot.21379openalex-snapshot
Computational sidechain placement and protein mutagenesis with implicit solvent models
inferred← citeshttps://doi.org/10.1002/prot.21395openalex-snapshot
Comparison between computational alanine scanning and per‐residue binding free energy decomposition for protein–protein association using MM‐GBSA: Application to the TCR‐p‐MHC complex
inferred← citeshttps://doi.org/10.1002/prot.21396openalex-snapshot
Hot spots—A review of the protein–protein interface determinant amino‐acid residues
inferred← citeshttps://doi.org/10.1002/prot.21661openalex-snapshot
Molecular dynamics simulation study for LRH‐1: Interaction with fragments of SHP and function of phospholipid ligand
inferred← citeshttps://doi.org/10.1002/prot.21834openalex-snapshot
Probing electrostatic interactions and ligand binding in aspartyl‐tRNA synthetase through site‐directed mutagenesis and computer simulations
inferred← citeshttps://doi.org/10.1002/prot.21844openalex-snapshot
A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect
inferred← citeshttps://doi.org/10.1002/prot.22687openalex-snapshot
Absolute binding free energy calculations: On the accuracy of computational scoring of protein–ligand interactions
inferred← citeshttps://doi.org/10.1002/prot.23042openalex-snapshot
Computational protein design with a generalized born solvent model: Application to asparaginyl‐tRNA synthetase
inferred← citeshttps://doi.org/10.1002/prot.24023openalex-snapshot
Conformational selection through electrostatics: Free energy simulations of gtp and gdp binding to archaeal initiation factor 2
inferred← citeshttps://doi.org/10.1002/prot.24158openalex-snapshot
Nucleotide recognition by the initiation factor aIF5B: Free energy simulations of a neoclassical GTPase
inferred← citeshttps://doi.org/10.1002/prot.25030openalex-snapshot
Protein side chain conformation predictions with an MMGBSA energy function
inferred← citeshttps://doi.org/10.1002/wcms.1157openalex-snapshot
Frontiers in free‐energy calculations of biological systems
inferred← citeshttps://doi.org/10.1007/0-387-23690-2_1openalex-snapshot
Organized Assemblies Probed by Fluorescence Spectroscopy
inferred← citeshttps://doi.org/10.1007/1-4020-5372-x_6openalex-snapshot
Computational Determination of the Relative Free Energy of Binding – Application to Alanine Scanning Mutagenesis
inferred← citeshttps://doi.org/10.1007/3-540-31618-3_12openalex-snapshot
Free Energy Calculations in Biological Systems. How Useful Are They in Practice?
inferred← citeshttps://doi.org/10.1007/3-540-31618-3_2openalex-snapshot
Modeling and Simulation Based Approaches for Investigating Allosteric Regulation in Enzymes
inferred← citeshttps://doi.org/10.1007/3-540-35284-8_17openalex-snapshot
Drug-Target Binding Investigated by Quantum Mechanical/Molecular Mechanical (QM/MM) Methods
inferred← citeshttps://doi.org/10.1007/978-1-4020-4851-3_8openalex-snapshot
Molecular Dynamics Simulations and Free Energy Calculations on Protein-Nucleic Acid Complexes
inferred← citeshttps://doi.org/10.1007/978-1-4939-0354-2_19openalex-snapshot
Virtual High-Throughput Ligand Screening
inferred← citeshttps://doi.org/10.1007/978-1-59745-177-2_7openalex-snapshot
Free Energy Calculations Applied to Membrane Proteins
inferred← citeshttps://doi.org/10.1007/978-1-61779-031-7_13openalex-snapshot
Structure-Based Design of Light-Controlled Proteins
inferred← citeshttps://doi.org/10.1007/978-3-030-05282-9_5openalex-snapshot
In Silico Structure-Based Prediction of Receptor–Ligand Binding Affinity: Current Progress and Challenges
inferred← citeshttps://doi.org/10.1007/978-3-030-48283-1_5openalex-snapshot
Developing Kinase Inhibitors Using Computer-Aided Drug Design Approaches
inferred← citeshttps://doi.org/10.1007/978-3-319-27282-5_31openalex-snapshot
Applications of Computational Methods to Simulations of Proteins Dynamics
inferred← citeshttps://doi.org/10.1007/978-3-319-75732-2_5openalex-snapshot
Molecular Dynamics Simulation Approach to Investigate Dynamic Behaviour of System Through the Application of Newtonian Mechanics
inferred← citeshttps://doi.org/10.1007/978-3-540-38448-9_12openalex-snapshot
Free Energy Calculations: Approximate Methods for Biological Macromolecules
inferred← citeshttps://doi.org/10.1007/978-3-540-38448-9_13openalex-snapshot
Applications of Free Energy Calculations to Chemistry and Biology
inferred← citeshttps://doi.org/10.1007/978-3-540-38448-9_2openalex-snapshot
Calculating Free Energy Differences Using Perturbation Theory
inferred← citeshttps://doi.org/10.1007/978-3-642-02597-6_1openalex-snapshot
How Biomolecular Motors Work: Synergy Between Single Molecule Experiments and Single Molecule Simulations
inferred← citeshttps://doi.org/10.1007/978-90-481-3034-4_16openalex-snapshot
Challenges for Computer Simulations in Drug Design
inferred← citeshttps://doi.org/10.1007/978-94-007-0711-5_31openalex-snapshot
Applications of Computational Methods to Simulations of Proteins Dynamics
inferred← citeshttps://doi.org/10.1007/978-94-007-6169-8_31-2openalex-snapshot
Applications of Computational Methods to Simulations of Protein Dynamics
inferred← citeshttps://doi.org/10.1007/978-981-10-2502-0_7openalex-snapshot
Variational Methods for Biomolecular Modeling
inferred← citeshttps://doi.org/10.1007/bf02990895openalex-snapshot
Steered molecular dynamics simulations of protein-ligand interactions
inferred← citeshttps://doi.org/10.1007/s00214-009-0592-2openalex-snapshot
Ab initio and ABEEM/MM fluctuating charge model studies of dimethyl phosphate anion in a microhydrated environment
inferred← citeshttps://doi.org/10.1007/s00214-011-0931-yopenalex-snapshot
An atomistic model for simulations of nilotinib and nilotinib/kinase binding
inferred← citeshttps://doi.org/10.1007/s00249-013-0892-2openalex-snapshot
Study of base pair mutations in proline-rich homeodomain (PRH)–DNA complexes using molecular dynamics
inferred← citeshttps://doi.org/10.1007/s00249-014-0999-0openalex-snapshot
Free energy simulations of amylin I26P mutation in a lipid bilayer
inferred← citeshttps://doi.org/10.1007/s00894-010-0694-8openalex-snapshot
Binding Selectivity of RecA to a single stranded DNA, a computational approach
inferred← citeshttps://doi.org/10.1007/s00894-011-1288-9openalex-snapshot
Accurate prediction of the binding free energy and analysis of the mechanism of the interaction of replication protein A (RPA) with ssDNA
inferred← citeshttps://doi.org/10.1007/s00894-012-1450-zopenalex-snapshot
Understanding the molecular mechanism of the broad and potent neutralization of HIV-1 by antibody VRC01 from the perspective of molecular dynamics simulation and binding free energy calculations
inferred← citeshttps://doi.org/10.1007/s10822-009-9300-5openalex-snapshot
Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length
inferred← citeshttps://doi.org/10.1007/s10822-012-9546-1openalex-snapshot
A fragment-based approach to the SAMPL3 Challenge
inferred← citeshttps://doi.org/10.1007/s10953-018-0769-1openalex-snapshot
Toward Expanded Diversity of Host–Guest Interactions via Synthesis and Characterization of Cyclodextrin Derivatives
inferred← citeshttps://doi.org/10.1007/s12010-024-05110-2openalex-snapshot
Decoding Drug Discovery: Exploring A-to-Z In Silico Methods for Beginners
inferred← citeshttps://doi.org/10.1007/s12039-023-02187-wopenalex-snapshot
Computational study of p$$\varvec{K}_\text{a}$$ shift of aspartate residue in thioredoxin: role of conformational sampling
inferred← citeshttps://doi.org/10.1016/b978-0-08-055294-1.00096-9openalex-snapshot
Computational Methods Related to Reaction Chemistry
inferred← citeshttps://doi.org/10.1016/b978-0-12-803581-8.10216-4openalex-snapshot
3.13 Computational Methods Related to Molecular Structure and Reaction Chemistry of Biomaterials ☆
inferred← citeshttps://doi.org/10.1016/bs.mie.2016.05.016openalex-snapshot
QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes
inferred← citeshttps://doi.org/10.1016/bs.mie.2016.05.024openalex-snapshot
Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics Simulation
inferred← citeshttps://doi.org/10.1016/bs.mie.2016.05.045openalex-snapshot
Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins
inferred← citeshttps://doi.org/10.1016/bs.mie.2016.05.047openalex-snapshot
Simulating Nuclear and Electronic Quantum Effects in Enzymes
inferred← citeshttps://doi.org/10.1016/j.bbagen.2014.07.006openalex-snapshot
Electrostatic free energies in translational GTPases: Classic allostery and the rest
inferred← citeshttps://doi.org/10.1016/j.bbamem.2012.05.012openalex-snapshot
Antimicrobial selectivity based on zwitterionic lipids and underlying balance of interactions
inferred← citeshttps://doi.org/10.1016/j.bbrc.2006.09.059openalex-snapshot
Correct and incorrect nucleotide incorporation pathways in DNA polymerase β
inferred← citeshttps://doi.org/10.1016/j.biotechadv.2014.11.011openalex-snapshot
Enhanced sampling techniques in biomolecular simulations
inferred← citeshttps://doi.org/10.1016/j.bpc.2006.07.001openalex-snapshot
Exploration of the conformational space of myosin recovery stroke via molecular dynamics
inferred← citeshttps://doi.org/10.1016/j.bpj.2008.12.3952openalex-snapshot
Mechanism and Energetics of Charybdotoxin Unbinding from a Potassium Channel from Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1016/j.bpj.2009.08.050openalex-snapshot
Tetracycline-Tet Repressor Binding Specificity: Insights from Experiments and Simulations
inferred← citeshttps://doi.org/10.1016/j.bpj.2012.01.043openalex-snapshot
Free-Energy Simulations Reveal that Both Hydrophobic and Polar Interactions Are Important for Influenza Hemagglutinin Antibody Binding
inferred← citeshttps://doi.org/10.1016/j.bpj.2014.03.013openalex-snapshot
Binding and Channeling of Alternative Substrates in the Enzyme DmpFG: a Molecular Dynamics Study
inferred← citeshttps://doi.org/10.1016/j.bpj.2018.01.008openalex-snapshot
Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations
inferred← citeshttps://doi.org/10.1016/j.cell.2005.10.001openalex-snapshot
A Structure-Based Model for the Synthesis and Hydrolysis of ATP by F1-ATPase
inferred← citeshttps://doi.org/10.1016/j.chemphys.2005.07.038openalex-snapshot
Direct correlation functions and the density functional theory of polar solvents
inferred← citeshttps://doi.org/10.1016/j.chphi.2021.100048openalex-snapshot
Role of molecular dynamics in optimising ligand discovery: Case study with novel inhibitor search for peptidyl t-RNA hydrolase
inferred← citeshttps://doi.org/10.1016/j.comptc.2014.03.034openalex-snapshot
Determinants of protein–ligand complex formation in the thyroid hormone receptor α: A molecular dynamics simulation study
inferred← citeshttps://doi.org/10.1016/j.cpc.2024.109125openalex-snapshot
Optimized parallelization of boundary integral Poisson-Boltzmann solvers
inferred← citeshttps://doi.org/10.1016/j.cplett.2006.05.062openalex-snapshot
A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations
inferred← citeshttps://doi.org/10.1016/j.cplett.2015.01.054openalex-snapshot
Quantum chemical approach for condensed-phase thermochemistry (II): Applications to formation and combustion reactions of liquid organic molecules
inferred← citeshttps://doi.org/10.1016/j.febslet.2005.10.031openalex-snapshot
An all atom energy based computational protocol for predicting binding affinities of protein–ligand complexes
inferred← citeshttps://doi.org/10.1016/j.fluid.2009.11.022openalex-snapshot
Molecular simulation of the hydration Gibbs energy of barbiturates
inferred← citeshttps://doi.org/10.1016/j.jcp.2018.07.011openalex-snapshot
On preconditioning the treecode-accelerated boundary integral (TABI) Poisson–Boltzmann solver
inferred← citeshttps://doi.org/10.1016/j.jmb.2006.11.095openalex-snapshot
Beyond Dimerization: A Membrane-dependent Activation Model for Interleukin-4 Receptor-mediated Signalling
inferred← citeshttps://doi.org/10.1016/j.jmb.2007.06.003openalex-snapshot
Affinity and Specificity of Protein U1A-RNA Complex Formation Based on an Additive Component Free Energy Model
inferred← citeshttps://doi.org/10.1016/j.jmb.2008.03.022openalex-snapshot
Tet Repressor Induction by Tetracycline: A Molecular Dynamics, Continuum Electrostatics, and Crystallographic Study
inferred← citeshttps://doi.org/10.1016/j.jmgm.2015.01.009openalex-snapshot
Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets
inferred← citeshttps://doi.org/10.1016/j.jmgm.2016.11.007openalex-snapshot
Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics
inferred← citeshttps://doi.org/10.1016/j.molcatb.2011.11.020openalex-snapshot
Contribution of both catalytic constant and Michaelis constant to CALB enantioselectivity: Use of FEP calculations for prediction studies
inferred← citeshttps://doi.org/10.1016/j.pbiomolbio.2014.05.004openalex-snapshot
Prediction and redesign of protein–protein interactions
inferred← citeshttps://doi.org/10.1016/j.sbi.2005.03.001openalex-snapshot
Enhancing the accuracy, the efficiency and the scope of free energy simulations
inferred← citeshttps://doi.org/10.1016/j.str.2006.08.013openalex-snapshot
Pheromone Discrimination by the Pheromone-Binding Protein of Bombyx mori
inferred← citeshttps://doi.org/10.1016/j.theochem.2007.04.012openalex-snapshot
Large-scale molecular dynamics of a G protein-coupled receptor, the human 5-HT4 serotonin receptor, in a lipid bilayer
inferred← citeshttps://doi.org/10.1016/j.theochem.2009.05.019openalex-snapshot
Studies on the torsions of nucleic acids using ABEEMσπ/MM method
inferred← citeshttps://doi.org/10.1016/s0006-3495(04)74084-9openalex-snapshot
Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy
inferred← citeshttps://doi.org/10.1016/s0009-2614(03)01057-1openalex-snapshot
Generalized ensembles serve to improve the convergence of free energy simulations
inferred← citeshttps://doi.org/10.1016/s0022-2836(03)00995-1openalex-snapshot
Rearrangement of Charge–Charge Interactions in Variant Ubiquitins as Detected by Double-Mutant Cycles and NMR
inferred← citeshttps://doi.org/10.1016/s0065-3160(03)38006-2openalex-snapshot
Computational Studies on the Mechanism of Orotidine Monophosphate Decarboxylase
inferred← citeshttps://doi.org/10.1016/s0301-4622(02)00293-4openalex-snapshot
Thermodynamics of protein folding: a microscopic view
inferred← citeshttps://doi.org/10.1016/s1574-1400(10)06003-2openalex-snapshot
Computing Free-Energy Profiles Using Multidimensional Potentials of Mean Force and Polynomial Quadrature Methods
inferred← citeshttps://doi.org/10.1016/s1574-1400(10)06004-4openalex-snapshot
QM/MM Alchemical Free Energy Simulations: Challenges and Recent Developments
inferred← citeshttps://doi.org/10.1021/acs.chemrev.5c00931openalex-snapshot
Uncertainty Quantification for In Silico Chemistry
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00411openalex-snapshot
Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01629openalex-snapshot
Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00564openalex-snapshot
Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00785openalex-snapshot
Accounting for the Central Role of Interfacial Water in Protein–Ligand Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00808openalex-snapshot
Dividing the Periodic Box into Subdivisions with Their Surroundings to Accelerate Molecular Dynamics Simulation with High Accuracy
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00591openalex-snapshot
Accurate and Efficient Multilevel Free Energy Simulations with Neural Network-Assisted Enhanced Sampling
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00407openalex-snapshot
Rapid, Accurate, Ranking of Protein–Ligand Binding Affinities with VM2, the Second-Generation Mining Minima Method
inferred← citeshttps://doi.org/10.1021/acs.jctc.5b00953openalex-snapshot
Predictive Sampling of Rare Conformational Events in Aqueous Solution: Designing a Generalized Orthogonal Space Tempering Method
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c00123openalex-snapshot
Isotropic Periodic Sum for Polarizable Gaussian Multipole Model
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b00470openalex-snapshot
Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b00202openalex-snapshot
Full Protein Sequence Redesign with an MMGBSA Energy Function
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00725openalex-snapshot
CL-FEP: An End-State Free Energy Perturbation Approach
inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c11321openalex-snapshot
An Active Site Inhibitor Induces Conformational Penalties for ACE2 Recognition by the Spike Protein of SARS-CoV-2
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c05480openalex-snapshot
Force Fields for Deep Eutectic Mixtures: Application to Structure, Thermodynamics and 2D-Infrared Spectroscopy
inferred← citeshttps://doi.org/10.1021/acs.jpcb.5b02810openalex-snapshot
Interplay of Electrostatics and Hydrophobic Effects in the Metamorphic Protein Human Lymphotactin
inferred← citeshttps://doi.org/10.1021/acs.jpcb.5c04731openalex-snapshot
The Dawn of Alchemical Free-Energy Methods in Biomolecular Simulations
inferred← citeshttps://doi.org/10.1021/acs.jpcc.5b05722openalex-snapshot
Enhanced Ab Initio Molecular Dynamics Simulation of the Temperature-Dependent Thermodynamics for the Diffusion of Carbon Monoxide on Ru(0001) Surface
inferred← citeshttps://doi.org/10.1021/acs.jpclett.5c01786openalex-snapshot
NMR-Derived Salt Bridges in Insulin Analogue: Resolving Artifactual Overbinding in Molecular Dynamics via Charge Scaling
inferred← citeshttps://doi.org/10.1021/ar010014popenalex-snapshot
Ligand Binding Affinities from MD Simulations
inferred← citeshttps://doi.org/10.1021/bi061061yopenalex-snapshot
Implications of Alternative Substrate Binding Modes for Catalysis by Uracil-DNA Glycosylase: An Apparent Discrepancy Resolved
inferred← citeshttps://doi.org/10.1021/bi201675nopenalex-snapshot
Conformational Selection by the aIF2 GTPase: A Molecular Dynamics Study of Functional Pathways
inferred← citeshttps://doi.org/10.1021/bi401126zopenalex-snapshot
Hemoglobin Bohr Effects: Atomic Origin of the Histidine Residue Contributions
inferred← citeshttps://doi.org/10.1021/bi801239uopenalex-snapshot
Computer Simulations Reveal a Novel Nucleotide-Type Binding Orientation for Ellipticine-Based Anticancer c-kit Kinase Inhibitors
inferred← citeshttps://doi.org/10.1021/bi801726qopenalex-snapshot
Binding of Tetracyclines to Elongation Factor Tu, the Tet Repressor, and the Ribosome: A Molecular Dynamics Simulation Study
inferred← citeshttps://doi.org/10.1021/bk-2021-1397.ch001openalex-snapshot
Free Energy Methods in Drug Discovery—Introduction
inferred← citeshttps://doi.org/10.1021/ci050141qopenalex-snapshot
A Comparative Study on the Application of Hierarchical−Agglomerative Clustering Approaches to Organize Outputs of Reiterated Docking Runs
inferred← citeshttps://doi.org/10.1021/ci2000874openalex-snapshot
Structural Basis for the β-Adrenergic Receptor Subtype Selectivity of the Representative Agonists and Antagonists
inferred← citeshttps://doi.org/10.1021/ci3003254openalex-snapshot
Correlating Protein Hot Spot Surface Analysis Using ProBiS with Simulated Free Energies of Protein–Protein Interfacial Residues
inferred← citeshttps://doi.org/10.1021/ci300385hopenalex-snapshot
Molecular Dynamics Investigation on a Series of HIV Protease Inhibitors: Assessing the Performance of MM-PBSA and MM-GBSA Approaches
inferred← citeshttps://doi.org/10.1021/ci4002102openalex-snapshot
A Contribution to the Drug Resistance Mechanism of Darunavir, Amprenavir, Indinavir, and Saquinavir Complexes with HIV-1 Protease Due to Flap Mutation I50V: A Systematic MM–PBSA and Thermodynamic Integration Study
inferred← citeshttps://doi.org/10.1021/ci600406vopenalex-snapshot
Solvated Interaction Energy (SIE) for Scoring Protein−Ligand Binding Affinities. 1. Exploring the Parameter Space
inferred← citeshttps://doi.org/10.1021/ci800004wopenalex-snapshot
MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization
inferred← citeshttps://doi.org/10.1021/ci900248fopenalex-snapshot
jSimMacs for GROMACS: A Java Application for Advanced Molecular Dynamics Simulations with Remote Access Capability
inferred← citeshttps://doi.org/10.1021/ci900497dopenalex-snapshot
Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations
inferred← citeshttps://doi.org/10.1021/cr040426mopenalex-snapshot
Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
inferred← citeshttps://doi.org/10.1021/cr500628bopenalex-snapshot
Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States
inferred← citeshttps://doi.org/10.1021/ct0499480openalex-snapshot
Hierarchical Numerical Solution of Smoluchowski Equations with Rough Potentials
inferred← citeshttps://doi.org/10.1021/ct0500904openalex-snapshot
Evaluating the Accuracy of the Quasiharmonic Approximation
inferred← citeshttps://doi.org/10.1021/ct100033sopenalex-snapshot
Practically Efficient QM/MM Alchemical Free Energy Simulations: The Orthogonal Space Random Walk Strategy
inferred← citeshttps://doi.org/10.1021/ct1002913openalex-snapshot
Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein−Ligand Binding Affinities
inferred← citeshttps://doi.org/10.1021/ct200061ropenalex-snapshot
Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics
inferred← citeshttps://doi.org/10.1021/ct200244popenalex-snapshot
A Direct Comparison of the MM-GB/SA Scoring Procedure and Free-Energy Perturbation Calculations Using Carbonic Anhydrase as a Test Case: Strengths and Pitfalls of Each Approach
inferred← citeshttps://doi.org/10.1021/ct200565uopenalex-snapshot
Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model
inferred← citeshttps://doi.org/10.1021/ct200623bopenalex-snapshot
On the Use of Enveloping Distribution Sampling (EDS) to Compute Free Enthalpy Differences between Different Conformational States of Molecules: Application to 310-, α-, and π-Helices
inferred← citeshttps://doi.org/10.1021/ct200726vopenalex-snapshot
Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering
inferred← citeshttps://doi.org/10.1021/ct300090zopenalex-snapshot
Alchemical Free Energy Differences in Flexible Molecules from Thermodynamic Integration or Free Energy Perturbation Combined with Driven Adiabatic Dynamics
inferred← citeshttps://doi.org/10.1021/ct300242fopenalex-snapshot
A Toolkit for the Analysis of Free-Energy Perturbation Calculations
inferred← citeshttps://doi.org/10.1021/ct500195popenalex-snapshot
An Overview of Electrostatic Free Energy Computations for Solutions and Proteins
inferred← citeshttps://doi.org/10.1021/ct500200nopenalex-snapshot
Relative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method
inferred← citeshttps://doi.org/10.1021/ct500571kopenalex-snapshot
MoD-QM/MM Structural Refinement Method: Characterization of Hydrogen Bonding in the Oxytricha nova G-Quadruplex
inferred← citeshttps://doi.org/10.1021/ct700121nopenalex-snapshot
Coarse-Graining the Accessible Surface and the Electrostatics of Proteins for Protein−Protein Interactions
inferred← citeshttps://doi.org/10.1021/ct700132wopenalex-snapshot
Recipe of Polarized One-Electron Potential Optimization for Development of Polarizable Force Fields
inferred← citeshttps://doi.org/10.1021/ct700151xopenalex-snapshot
Coarse-Grained Protein Model Coupled with a Coarse-Grained Water Model: Molecular Dynamics Study of Polyalanine-Based Peptides
inferred← citeshttps://doi.org/10.1021/ct700245aopenalex-snapshot
A Combined QM/MM Poisson−Boltzmann Approach
inferred← citeshttps://doi.org/10.1021/ct800160qopenalex-snapshot
Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations
inferred← citeshttps://doi.org/10.1021/ct8003707openalex-snapshot
MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein−Protein Interface
inferred← citeshttps://doi.org/10.1021/ct9006597openalex-snapshot
Evaluations of the Absolute and Relative Free Energies for Antidepressant Binding to the Amino Acid Membrane Transporter LeuT with Free Energy Simulations
inferred← citeshttps://doi.org/10.1021/ic034281yopenalex-snapshot
Uranyl and Strontium Salt Solvation in Room-Temperature Ionic Liquids. A Molecular Dynamics Investigation
inferred← citeshttps://doi.org/10.1021/ja072905jopenalex-snapshot
Relative Binding Affinities of Fructose-1,6-Bisphosphatase Inhibitors Calculated Using a Quantum Mechanics-Based Free Energy Perturbation Method
inferred← citeshttps://doi.org/10.1021/ja0741933openalex-snapshot
Molecular Dynamics Simulations of the 30S Ribosomal Subunit Reveal a Preferred Tetracycline Binding Site
inferred← citeshttps://doi.org/10.1021/ja103742kopenalex-snapshot
Electronic Properties and Desolvation Penalties of Metal Ions Plus Protein Electrostatics Dictate the Metal Binding Affinity and Selectivity in the Copper Efflux Regulator
inferred← citeshttps://doi.org/10.1021/ja2069104openalex-snapshot
Extension of Marcus Picture for Electron Transfer Reactions with Large Solvation Changes
inferred← citeshttps://doi.org/10.1021/ja304601kopenalex-snapshot
The Catalytic Mechanism of HIV-1 Integrase for DNA 3′-End Processing Established by QM/MM Calculations
inferred← citeshttps://doi.org/10.1021/ja904951topenalex-snapshot
Importance of Charge Independent Effects in Readout of the Trimethyllysine Mark by HP1 Chromodomain
inferred← citeshttps://doi.org/10.1021/jm060522aopenalex-snapshot
Accurate Prediction of the Relative Potencies of Members of a Series of Kinase Inhibitors Using Molecular Docking and MM-GBSA Scoring
inferred← citeshttps://doi.org/10.1021/jm0608457openalex-snapshot
Stereoselectivity by Enantiomeric Inhibitors of Matrix Metalloproteinase-8: New Insights from Molecular Dynamics Simulations
showing the first 200 of 366 · page through all 366
Editorial review for independent work. ICSAC — the Institute for Complexity
Science and Advanced Computing — runs a structured editorial panel for researchers
publishing outside journals, and publishes on CiteStamp rails. Submission is free
and goes through ORCID: icsacinstitute.org/submit.