Comparative study of generalized Born models: protein dynamics.
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.
Fan
Hao
H
Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
Mark
Alan E
AE
Zhu
Jiang
J
Honig
Barry
B
D000704:Analysis of Variance; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D006801:Humans; D006860:Hydrogen Bonding; D046911:Macromolecular Substances; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008962:Models, Theoretical; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013816:Thermodynamics; D014764:Viral Proteins / Q000737:chemistry
D001426:Bacterial Proteins; D046911:Macromolecular Substances; D011506:Proteins; D014764:Viral Proteins