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Items: 1 to 20 of 118

1.

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
2.

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
3.

Application of Markov State Models to simulate long timescale dynamics of biological macromolecules.

Da LT, Sheong FK, Silva DA, Huang X.

Adv Exp Med Biol. 2014;805:29-66. doi: 10.1007/978-3-319-02970-2_2.

PMID:
24446356
4.

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.

Molloy K, Shehu A.

BMC Struct Biol. 2013;13 Suppl 1:S8. doi: 10.1186/1472-6807-13-S1-S8. Epub 2013 Nov 8.

5.

Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes.

Zimmerman MI, Porter JR, Sun X, Silva RR, Bowman GR.

J Chem Theory Comput. 2018 Nov 13;14(11):5459-5475. doi: 10.1021/acs.jctc.8b00500. Epub 2018 Oct 23.

PMID:
30240203
6.

Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms.

Huang X, Yao Y, Bowman GR, Sun J, Guibas LJ, Carlsson G, Pande VS.

Pac Symp Biocomput. 2010:228-39.

7.

Extensive conformational heterogeneity within protein cores.

Bowman GR, Geissler PL.

J Phys Chem B. 2014 Jun 19;118(24):6417-23. doi: 10.1021/jp4105823. Epub 2014 Mar 12.

8.

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
9.

Markov state models provide insights into dynamic modulation of protein function.

Shukla D, Hernández CX, Weber JK, Pande VS.

Acc Chem Res. 2015 Feb 17;48(2):414-22. doi: 10.1021/ar5002999. Epub 2015 Jan 3. Review.

10.

Simple, yet powerful methodologies for conformational sampling of proteins.

Harada R, Takano Y, Baba T, Shigeta Y.

Phys Chem Chem Phys. 2015 Mar 7;17(9):6155-73. doi: 10.1039/c4cp05262e.

PMID:
25659594
11.

From thermodynamics to kinetics: enhanced sampling of rare events.

Yang L, Liu CW, Shao Q, Zhang J, Gao YQ.

Acc Chem Res. 2015 Apr 21;48(4):947-55. doi: 10.1021/ar500267n. Epub 2015 Mar 17. Review.

PMID:
25781363
12.

Using robotics to fold proteins and dock ligands.

Brutlag D, Apaydin S, Guestrin C, Hsu D, Varma C, Singh A, Latombe JC.

Bioinformatics. 2002;18 Suppl 2:S74.

PMID:
12385986
13.

Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands.

Zhang L, Jiang H, Sheong FK, Pardo-Avila F, Cheung PP, Huang X.

Methods Enzymol. 2016;578:343-71. doi: 10.1016/bs.mie.2016.05.026. Epub 2016 Jun 24. Review.

PMID:
27497174
14.

Efficient traversal of beta-sheet protein folding pathways using ensemble models.

Shenker S, O'Donnell CW, Devadas S, Berger B, Waldispühl J.

J Comput Biol. 2011 Nov;18(11):1635-47. doi: 10.1089/cmb.2011.0176. Epub 2011 Sep 29.

PMID:
21958108
15.

SIMS: a hybrid method for rapid conformational analysis.

Gipson B, Moll M, Kavraki LE.

PLoS One. 2013 Jul 23;8(7):e68826. doi: 10.1371/journal.pone.0068826. Print 2013.

16.

Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: application to the folding of a mini-protein, chignolin.

Harada R, Takano Y, Shigeta Y.

J Comput Chem. 2015 Apr 15;36(10):763-72. doi: 10.1002/jcc.23854. Epub 2015 Feb 18.

PMID:
25691321
17.

Thermodynamics and kinetics of large-time-step molecular dynamics.

Rao F, Spichty M.

J Comput Chem. 2012 Feb 15;33(5):475-83. doi: 10.1002/jcc.21990. Epub 2011 Dec 19.

PMID:
22180257
18.
19.

Conformation spaces of proteins.

Sullivan DC, Kuntz ID.

Proteins. 2001 Mar 1;42(4):495-511.

PMID:
11170204
20.

Hierarchical Nyström methods for constructing Markov state models for conformational dynamics.

Yao Y, Cui RZ, Bowman GR, Silva DA, Sun J, Huang X.

J Chem Phys. 2013 May 7;138(17):174106. doi: 10.1063/1.4802007.

PMID:
23656113

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