Treating entropy and conformational changes in implicit solvent simulations of small molecules

scientific article published on 3 January 2008

Treating entropy and conformational changes in implicit solvent simulations of small molecules is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1021/JP0764384
P932PMC publication ID2745223
P698PubMed publication ID18171044
P5875ResearchGate publication ID5678827

P50authorKen A. DillQ6387211
John D. ChoderaQ41044041
David L. MobleyQ55143475
P2860cites workThe Amber biomolecular simulation programsQ27860745
Scoring a diverse set of high-quality docked conformations: a metascore based on electrostatic and desolvation interactionsQ28299530
Development and testing of a general amber force fieldQ29547642
Exploring protein native states and large-scale conformational changes with a modified generalized born modelQ29617088
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validationQ29617869
Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymesQ30160326
Protein folding by zipping and assemblyQ30362818
bcl::Cluster : A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics SystemQ30394944
Generalized born models of macromolecular solvation effectsQ34059768
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computingQ34176555
Generalized Born model with a simple, robust molecular volume correctionQ34287102
Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume termsQ34694062
Ligand configurational entropy and protein bindingQ35607011
Estimation of Absolute Free Energies of Hydration Using Continuum Methods:  Accuracy of Partial Charge Models and Optimization of Nonpolar ContributionsQ44854320
Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies:  Lessons Learned with Atom-Centered Dielectric Functions.Q45986689
Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screeningQ46135091
Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.Q46136993
Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force FieldQ46225929
Assessing scoring functions for protein-ligand interactionsQ47429905
The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.Q48640184
The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers.Q49315995
Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.Q51633889
A new method for computing the macromolecular electric potential.Q51658612
Ligand solvation in molecular docking.Q52214239
Energetics of charge-charge interactions in proteins.Q52427206
AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.Q54640063
SM6: A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute−Water ClustersQ57250573
Calculation of the electric potential in the active site cleft due to alpha-helix dipolesQ72952190
Beta-hairpin folding simulations in atomistic detail using an implicit solvent modelQ74621827
Theory and applications of the generalized Born solvation model in macromolecular simulationsQ77381573
Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood MethodsQ79283802
Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residuesQ79461109
Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water modelsQ80189502
P433issue3
P407language of work or nameEnglishQ1860
P304page(s)938-946
P577publication date2008-01-03
P1433published inJournal of Physical Chemistry BQ668669
P1476titleTreating entropy and conformational changes in implicit solvent simulations of small molecules
P478volume112

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cites work (P2860)
Q47567527Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.
Q39343604Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities
Q41900473Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions.
Q43078853Analysis of SM8 and Zap TK calculations and their geometric sensitivity
Q46105073Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database
Q41958867Assessing the performance of implicit solvation models at a nucleic acid surface
Q34537730Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes
Q39248732Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies.
Q37372747Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".
Q57274992Biological applications of classical electrostatics methods
Q42557446Charge asymmetries in hydration of polar solutes.
Q47437776Comparative Assessment of Computational Methods for Free Energy Calculations of Ionic Hydration
Q37607031Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method
Q42410027Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies
Q57905894Dependency of ligand free energy landscapes on charge parameters and solvent models
Q35041180Differential geometry based solvation model II: Lagrangian formulation
Q39721704Evaluating the dynamics and electrostatic interactions of folded proteins in implicit solvents
Q39422903Fast and accurate generation of ab initio quality atomic charges using nonparametric statistical regression
Q40942296Field-SEA: a model for computing the solvation free energies of nonpolar, polar, and charged solutes in water
Q28655211FreeSolv: a database of experimental and calculated hydration free energies, with input files
Q48894752Generalized Born implicit solvent models for small molecule hydration free energies.
Q26998920Global analysis of riboswitches by small-angle X-ray scattering and calorimetry
Q45064927Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies
Q38088365High-throughput and in silico screenings in drug discovery.
Q47793987How accurate are continuum solvation models for drug-like molecules?
Q58982515How accurate are the popular PCM/GB continuum solvation models for calculating the solvation energies of amino acid side-chain analogs?
Q33640094Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans
Q38732734Introducing Charge Hydration Asymmetry into the Generalized Born Model
Q30410587Lead optimization mapper: automating free energy calculations for lead optimization
Q37701502Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes
Q30394968Nonlocal Electrostatics in Spherical Geometries Using Eigenfunction Expansions of Boundary-Integral Operators
Q30538681On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi
Q36628360Parameterization of a geometric flow implicit solvation model
Q84014403Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations
Q30766874Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field.
Q37761334Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations
Q43124392Predictions of hydration free energies from all-atom molecular dynamics simulations.
Q43114172Predictions of hydration free energies from continuum solvent with solute polarizable models: the SAMPL2 blind challenge
Q28817868Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation
Q44262192Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge
Q90878673Reparametrization of the COSMO Solvent Model for Semiempirical Methods PM6 and PM7
Q43107625SAMPL2 and continuum modeling
Q45975662SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling.
Q39638964Small molecule hydration energy and entropy from 3D-RISM.
Q39901298Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations
Q33953525Surveying implicit solvent models for estimating small molecule absolute hydration free energies
Q33803629The AGBNP2 Implicit Solvation Model.
Q34352706The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities

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