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-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.
Marelius
J
J
Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Sweden.
Kolmodin
K
K
Feierberg
I
I
Aqvist
J
J
D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D008024:Ligands; D046911:Macromolecular Substances; D008958:Models, Molecular; D009154:Mutation; D011485:Protein Binding; D017027:Protein Tyrosine Phosphatases / Q000737:chemistry*; D012984:Software; D055672:Static Electricity; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D008024:Ligands; D046911:Macromolecular Substances; D014867:Water; D017027:Protein Tyrosine Phosphatases