Comparative study of generalized Born models: Protein dynamics
Open Access
- 6 April 2005
- journal article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 102 (19) , 6760-6764
- https://doi.org/10.1073/pnas.0408857102
Abstract
In this work, we compare the results of molecular dynamics simulations involving the application of three generalized Born (GB) models to 10 different proteins. The three GB models, the Still, HCT, and modified analytical generalized Born models, were implemented in the computationally efficient gromacs package. The performance of each model was assessed from the backbone rms deviation from the native structure, the number of native hydrogen bonds retained in the simulation, and the experimental and calculated radius of gyration. Analysis of variance (ANOVA) was used to analyze the results of the simulations. The rms deviation measure was found to be unable to distinguish the quality of the results obtained with the three different GB models, whereas the number of native hydrogen bonds and radius of gyration yielded a statistically meaningful discrimination among models. Our results suggest that, of the three, modified analytical generalized Born yields the best agreement between calculated and experimentally derived structures. More generally, our study highlights the need both to evaluate the effects of different variables on the results of simulations and to verify that the results of molecular dynamics simulations are statistically meaningful.Keywords
This publication has 25 references indexed in Scilit:
- Relative stability of protein structures determined by X‐ray crystallography or NMR spectroscopy: A molecular dynamics simulation studyProteins-Structure Function and Bioinformatics, 2003
- Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimerJournal of Computational Chemistry, 2003
- Molecular dynamics of biological macromolecules: A brief history and perspectiveBiopolymers, 2003
- Corrigenda: Molecular dynamics simulations of biomoleculesNature Structural & Molecular Biology, 2002
- Effective Born radii in the generalized Born approximation: The importance of being perfectJournal of Computational Chemistry, 2002
- Parametrization of a Generalized Born/Solvent-Accessible Surface Area Model and Applications to the Simulation of Protein DynamicsThe Journal of Physical Chemistry B, 2002
- Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objectsJournal of Computational Chemistry, 2001
- An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous SolutionJournal of Molecular Biology, 1996
- GROMACS: A message-passing parallel molecular dynamics implementationComputer Physics Communications, 1995
- Solvent accessible surface area and excluded volume in proteinsJournal of Molecular Biology, 1984