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Items: 1 to 20 of 101

1.

Learning generative models of molecular dynamics.

Razavian NS, Kamisetty H, Langmead CJ.

BMC Genomics. 2012;13 Suppl 1:S5. doi: 10.1186/1471-2164-13-S1-S5. Epub 2012 Jan 17.

2.

Learning generative models for protein fold families.

Balakrishnan S, Kamisetty H, Carbonell JG, Lee SI, Langmead CJ.

Proteins. 2011 Apr;79(4):1061-78. doi: 10.1002/prot.22934. Epub 2011 Jan 25.

PMID:
21268112
3.

A Bayesian method for construction of Markov models to describe dynamics on various time-scales.

Rains EK, Andersen HC.

J Chem Phys. 2010 Oct 14;133(14):144113. doi: 10.1063/1.3496438.

PMID:
20949993
5.

Effect of Clustering Algorithm on Establishing Markov State Model for Molecular Dynamics Simulations.

Li Y, Dong Z.

J Chem Inf Model. 2016 Jun 27;56(6):1205-15. doi: 10.1021/acs.jcim.6b00181. Epub 2016 Jun 8.

PMID:
27249546
6.

Generative models of conformational dynamics.

Langmead CJ.

Adv Exp Med Biol. 2014;805:87-105. doi: 10.1007/978-3-319-02970-2_4. Review.

7.

FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs.

Zimmerman MI, Bowman GR.

J Chem Theory Comput. 2015 Dec 8;11(12):5747-57. doi: 10.1021/acs.jctc.5b00737. Epub 2015 Nov 20.

PMID:
26588361
8.

A hidden markov model derived structural alphabet for proteins.

Camproux AC, Gautier R, Tufféry P.

J Mol Biol. 2004 Jun 4;339(3):591-605.

PMID:
15147844
9.

Conditional graphical models for protein structural motif recognition.

Liu Y, Carbonell J, Gopalakrishnan V, Weigele P.

J Comput Biol. 2009 May;16(5):639-57. doi: 10.1089/cmb.2008.0176.

PMID:
19432536
10.

Validating clustering of molecular dynamics simulations using polymer models.

Phillips JL, Colvin ME, Newsam S.

BMC Bioinformatics. 2011 Nov 14;12:445. doi: 10.1186/1471-2105-12-445.

11.

Unbiased, scalable sampling of protein loop conformations from probabilistic priors.

Zhang Y, Hauser K.

BMC Struct Biol. 2013;13 Suppl 1:S9. doi: 10.1186/1472-6807-13-S1-S9. Epub 2013 Nov 8.

12.

Mixture models for protein structure ensembles.

Hirsch M, Habeck M.

Bioinformatics. 2008 Oct 1;24(19):2184-92. doi: 10.1093/bioinformatics/btn396. Epub 2008 Jul 28.

PMID:
18662925
13.

Sparse networks of directly coupled, polymorphic, and functional side chains in allosteric proteins.

Soltan Ghoraie L, Burkowski F, Zhu M.

Proteins. 2015 Mar;83(3):497-516. doi: 10.1002/prot.24752. Epub 2015 Jan 31.

PMID:
25545075
14.

Automatic state partitioning for multibody systems (APM): an efficient algorithm for constructing Markov state models to elucidate conformational dynamics of multibody systems.

Sheong FK, Silva DA, Meng L, Zhao Y, Huang X.

J Chem Theory Comput. 2015 Jan 13;11(1):17-27. doi: 10.1021/ct5007168. Epub 2014 Dec 23.

PMID:
26574199
15.

How to Run FAST Simulations.

Zimmerman MI, Bowman GR.

Methods Enzymol. 2016;578:213-25. doi: 10.1016/bs.mie.2016.05.032. Epub 2016 Jun 16. Review.

PMID:
27497168
16.

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint.

Bacallado S, Chodera JD, Pande V.

J Chem Phys. 2009 Jul 28;131(4):045106. doi: 10.1063/1.3192309.

17.

QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin.

Savol AJ, Burger VM, Agarwal PK, Ramanathan A, Chennubhotla CS.

Bioinformatics. 2011 Jul 1;27(13):i52-60. doi: 10.1093/bioinformatics/btr248.

18.

Molecular dynamics study of naturally existing cavity couplings in proteins.

Barbany M, Meyer T, Hospital A, Faustino I, D'Abramo M, Morata J, Orozco M, de la Cruz X.

PLoS One. 2015 Mar 27;10(3):e0119978. doi: 10.1371/journal.pone.0119978. eCollection 2015.

19.
20.

Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

Taly JF, Marin A, Gibrat JF.

BMC Bioinformatics. 2008 Jan 7;9:6. doi: 10.1186/1471-2105-9-6.

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