Advances in free-energy-based simulations of protein folding and ligand binding.

scientific article

Advances in free-energy-based simulations of protein folding and ligand binding. is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1016/J.SBI.2015.12.002
P932PMC publication ID4785060
P698PubMed publication ID26773233
P5875ResearchGate publication ID289569007

P50authorKen A. DillQ6387211
Alberto PerezQ63852517
P2093author name stringCarlos Simmerling
Joseph A Morrone
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Systematic validation of protein force fields against experimental dataQ28731830
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Improved protein-ligand docking using GOLDQ29616787
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Microsecond folding experiments and simulations: a match is madeQ36784578
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Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".Q37372747
Computational studies of protein aggregation: methods and applicationsQ38342958
ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of ProteinsQ39110778
How does a drug molecule find its target binding site?Q39280041
Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulationsQ39673202
New force field on modeling intrinsically disordered proteins.Q44063793
Scaling of folding times with protein sizeQ47395668
A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects.Q49086727
Calculation of Standard Binding Free Energies:  Aromatic Molecules in the T4 Lysozyme L99A MutantQ53190267
Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields.Q54267278
Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein StatesQ56873339
Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR StudyQ58062171
Balance between α and β Structures in Ab Initio Protein FoldingQ60490645
Free energy calculations by computer simulationQ69004087
Calculation of the relative change in binding free energy of a protein-inhibitor complexQ69736806
Protein dynamics in solution and in a crystalline environment: a molecular dynamics studyQ72669735
Visualizing the Induced Binding of SH2-PhosphopeptideQ86770910
Force Field for Peptides and Proteins based on the Classical Drude OscillatorQ30358273
The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational ChangeQ30372513
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.Q30372639
Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inferenceQ30375259
Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamicsQ30409188
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular SimulationQ30415382
Statistically optimal analysis of samples from multiple equilibrium statesQ30438437
Pathway and mechanism of drug binding to G-protein-coupled receptors.Q30503489
Solvent fluctuations in hydrophobic cavity-ligand binding kineticsQ30533272
Funnel metadynamics as accurate binding free-energy methodQ30539051
Phosphate release coupled to rotary motion of F1-ATPaseQ30551514
Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solventQ30591583
The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.Q30684750
Context-independent, temperature-dependent helical propensities for amino acid residuesQ33496223
Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptorQ33699049
Calculation of absolute protein-ligand binding free energy from computer simulationsQ33784404
Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit waterQ34032669
Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA.Q34044404
Drug-target residence time: critical information for lead optimization.Q34054343
Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptideQ34080081
How fast-folding proteins foldQ34228223
Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force fieldQ34459931
Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein AssociationQ34503099
Development and validation of a modular, extensible docking program: DOCK 5.Q34588100
COMPUTING: Screen Savers of the World Unite!Q34670167
Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting stepsQ35062738
Improved Generalized Born Solvent Model Parameters for Protein SimulationsQ35180754
Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolutionQ35372059
Mapping fast protein folding with multiple-site fluorescent probesQ35818750
Residue-specific α-helix propensities from molecular simulationQ35843475
Elasticity, friction, and pathway of γ-subunit rotation in FoF1-ATP synthaseQ36008252
Accelerating molecular simulations of proteins using Bayesian inference on weak information.Q36103048
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral anglesQ36546184
Drug-target residence time and its implications for lead optimizationQ36556505
P921main subjectprotein foldingQ847556
P304page(s)25-31
P577publication date2016-01-07
P1433published inCurrent Opinion in Structural BiologyQ15758416
P1476titleAdvances in free-energy-based simulations of protein folding and ligand binding
P478volume36

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