Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes

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Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes is …
instance of (P31):
scholarly articleQ13442814

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P8978DBLP publication IDjournals/jcc/KnightYB13
P356DOI10.1002/JCC.23199
P932PMC publication ID4402937
P698PubMed publication ID23292859

P2093author name stringCharles L Brooks
Joseph D Yesselman
Jennifer L Knight
P2860cites workCHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fieldsQ24632987
CHARMM: the biomolecular simulation programQ24658108
Development and testing of a general amber force fieldQ29547642
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validationQ29617869
Statistically optimal analysis of samples from multiple equilibrium statesQ30438437
Surveying implicit solvent models for estimating small molecule absolute hydration free energiesQ33953525
MATCH: an atom-typing toolset for molecular mechanics force fields.Q34063434
Recent advances in the development and application of implicit solvent models in biomolecule simulationsQ35749514
Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulationsQ39901298
Predicting small-molecule solvation free energies: an informal blind test for computational chemistryQ40131892
Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent ModelQ40272426
Treating entropy and conformational changes in implicit solvent simulations of small moleculesQ41870076
Estimation of Absolute Free Energies of Hydration Using Continuum Methods:  Accuracy of Partial Charge Models and Optimization of Nonpolar ContributionsQ44854320
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.Q45986592
Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.Q46136993
FACTS: Fast analytical continuum treatment of solvation.Q51904502
Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solutionQ52008690
Generalized born model with a simple smoothing function.Q52009475
CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsQ53340989
Semianalytical treatment of solvation for molecular mechanics and dynamicsQ56866446
A Blind Challenge for Computational Solvation Free Energies: Introduction and OverviewQ59795439
Functionality pattern matching as an efficient complementary structure/reaction search tool: an open-source approachQ84748533
Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force FieldQ86825224
P433issue11
P921main subjectCHARMMQ902642
P304page(s)893-903
P577publication date2013-01-07
P1433published inJournal of Computational ChemistryQ3186908
P1476titleAssessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes
P478volume34

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cites work (P2860)
Q37549101All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.
Q36539936CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.
Q41349313Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water.
Q46731467Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level
Q57815938Escaping atom types in force fields using direct chemical perception
Q28655211FreeSolv: a database of experimental and calculated hydration free energies, with input files
Q92786098Infinite Dilution Activity Coefficients as Constraints for Force Field Parametrization and Method Development
Q38129103Molecular mechanics
Q36711952Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors
Q41144268Parameterization of the Hamiltonian Dielectric Solvent (HADES) Reaction-Field Method for the Solvation Free Energies of Amino Acid Side-Chain Analogs
Q39054857Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models.
Q39054869Predicting hydrophobic solvation by molecular simulation: 2. New united-atom model for alkanes, alkenes, and alkynes.

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