Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems

A new molecular dynamics program for free energy calculations in biomolecular systems is presented. It is principally designed for free energy perturbation simulations, empirical valence bond calculations, and binding affinity estimation by linear interaction energy methods. Evaluation of ligand-bin...

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Published inJournal of molecular graphics & modelling Vol. 16; no. 4; pp. 213 - 225
Main Authors Marelius, John, Kolmodin, Karin, Feierberg, Isabella, Åqvist, Johan
Format Journal Article
LanguageEnglish
Published United States Elsevier Inc 01.08.1998
Subjects
Algorithms
Binding Sites
Computer Simulation
empirical valence bond method
free energy perturbation
Ligands
Macromolecular Substances
Models, Molecular
molecular dynamics
Mutation
Protein Binding
protein tyrosine phosphatases
Protein Tyrosine Phosphatases - chemistry
Software
Static Electricity
Thermodynamics
Water - chemistry
free energy perturbation
empirical valence bond method
molecular dynamics
protein tyrosine phosphatases
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Summary:A new molecular dynamics program for free energy calculations in biomolecular systems is presented. It is principally designed for free energy perturbation simulations, empirical valence bond calculations, and binding affinity estimation by linear interaction energy methods. Evaluation of ligand-binding selectivity and free energy profiles for nucleophile activation in two protein tyrosine phosphatases as well as absolute binding affinity estimation for a lysine-binding protein are given as examples.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
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ISSN:1093-3263
1873-4243
DOI:10.1016/S1093-3263(98)80006-5