Convergence of sampling in protein simulations - PubMed (original) (raw)
. 2002 Mar;65(3 Pt 1):031910.
doi: 10.1103/PhysRevE.65.031910. Epub 2002 Mar 1.
Affiliations
- PMID: 11909112
- DOI: 10.1103/PhysRevE.65.031910
Convergence of sampling in protein simulations
Berk Hess. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Mar.
Abstract
With molecular dynamics protein dynamics can be simulated in atomic detail. Current computers are not fast enough to probe all available conformations, but fluctuations around one conformation can be sampled to a reasonable extent. The motions with the largest fluctuations can be filtered out of a simulation using covariance or principal component analysis. A problem with this analysis is that random diffusion can appear as correlated motion. An analysis is presented of how long a simulation should be to obtain relevant results for global motions. The analysis reveals that the cosine content of the principal components is a good indicator for bad sampling.
Similar articles
- Can principal components yield a dimension reduced description of protein dynamics on long time scales?
Lange OF, Grubmüller H. Lange OF, et al. J Phys Chem B. 2006 Nov 16;110(45):22842-52. doi: 10.1021/jp062548j. J Phys Chem B. 2006. PMID: 17092036 - GRID-MD-A tool for massive simulation of protein channels.
Carrillo O, Orozco M. Carrillo O, et al. Proteins. 2008 Feb 15;70(3):892-9. doi: 10.1002/prot.21592. Proteins. 2008. PMID: 17803238 - Application of the multiensemble sampling to the equilibrium folding of proteins.
Son HS, Kim SY, Lee J, Han KK. Son HS, et al. Bioinformatics. 2006 Aug 1;22(15):1832-7. doi: 10.1093/bioinformatics/btl282. Epub 2006 Jun 9. Bioinformatics. 2006. PMID: 16766555 - Long-timescale molecular dynamics simulations of protein structure and function.
Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE. Klepeis JL, et al. Curr Opin Struct Biol. 2009 Apr;19(2):120-7. doi: 10.1016/j.sbi.2009.03.004. Epub 2009 Apr 8. Curr Opin Struct Biol. 2009. PMID: 19361980 Review. - Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations.
Piana S, Klepeis JL, Shaw DE. Piana S, et al. Curr Opin Struct Biol. 2014 Feb;24:98-105. doi: 10.1016/j.sbi.2013.12.006. Epub 2014 Jan 24. Curr Opin Struct Biol. 2014. PMID: 24463371 Review.
Cited by
- Immobilization of the N-terminal helix stabilizes prefusion paramyxovirus fusion proteins.
Song AS, Poor TA, Abriata LA, Jardetzky TS, Dal Peraro M, Lamb RA. Song AS, et al. Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):E3844-51. doi: 10.1073/pnas.1608349113. Epub 2016 Jun 22. Proc Natl Acad Sci U S A. 2016. PMID: 27335462 Free PMC article. - Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization.
Fahrenkamp D, Li J, Ernst S, Schmitz-Van de Leur H, Chatain N, Küster A, Koschmieder S, Lüscher B, Rossetti G, Müller-Newen G. Fahrenkamp D, et al. Sci Rep. 2016 Oct 18;6:35454. doi: 10.1038/srep35454. Sci Rep. 2016. PMID: 27752093 Free PMC article. - Combined Structural Analysis and Molecular Dynamics Reveal Penicillin-Binding Protein Inhibition Mode with β-Lactones.
Flanders PL, Contreras-Martel C, Brown NW, Shirley JD, Martins A, Nauta KN, Dessen A, Carlson EE, Ambrose EA. Flanders PL, et al. ACS Chem Biol. 2022 Nov 18;17(11):3110-3120. doi: 10.1021/acschembio.2c00503. Epub 2022 Sep 29. ACS Chem Biol. 2022. PMID: 36173746 Free PMC article. - Repurposing FDA-approved drugs as FXR agonists: a structure based in silico pharmacological study.
Jose S, Devi SS, Sajeev A, Girisa S, Alqahtani MS, Abbas M, Alshammari A, Sethi G, Kunnumakkara AB. Jose S, et al. Biosci Rep. 2023 Mar 31;43(3):BSR20212791. doi: 10.1042/BSR20212791. Biosci Rep. 2023. PMID: 35348180 Free PMC article. - The 3D structures of G-quadruplexes of HIV-1 integrase inhibitors: molecular dynamics simulations in aqueous solution and in the gas phase.
Li MH, Zhou YH, Luo Q, Li ZS. Li MH, et al. J Mol Model. 2010 Apr;16(4):645-57. doi: 10.1007/s00894-009-0592-0. Epub 2009 Oct 4. J Mol Model. 2010. PMID: 19802725
MeSH terms
Substances
LinkOut - more resources
Other Literature Sources
Research Materials