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Items: 1 to 20 of 110

1.

Hybrid approaches to molecular simulation.

Ho BK, Perahia D, Buckle AM.

Curr Opin Struct Biol. 2012 Jun;22(3):386-93. doi: 10.1016/j.sbi.2012.05.005. Epub 2012 May 25. Review.

PMID:
22633678
2.

Reaching biological timescales with all-atom molecular dynamics simulations.

Zwier MC, Chong LT.

Curr Opin Pharmacol. 2010 Dec;10(6):745-52. doi: 10.1016/j.coph.2010.09.008. Epub 2010 Oct 8. Review.

PMID:
20934381
3.

Frontiers in molecular dynamics simulations of DNA.

PĂ©rez A, Luque FJ, Orozco M.

Acc Chem Res. 2012 Feb 21;45(2):196-205. doi: 10.1021/ar2001217. Epub 2011 Aug 10. Review.

PMID:
21830782
4.

Long-timescale molecular dynamics simulations of protein structure and function.

Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE.

Curr Opin Struct Biol. 2009 Apr;19(2):120-7. doi: 10.1016/j.sbi.2009.03.004. Epub 2009 Apr 8. Review.

PMID:
19361980
5.

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
6.

Native structure-based modeling and simulation of biomolecular systems per mouse click.

Lutz B, Sinner C, Bozic S, Kondov I, Schug A.

BMC Bioinformatics. 2014 Aug 29;15:292. doi: 10.1186/1471-2105-15-292.

7.

Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions.

Bhattacharyya M, Vishveshwara S.

Mol Biosyst. 2011 Jul;7(7):2320-30. doi: 10.1039/c1mb05038a. Epub 2011 May 27.

PMID:
21617814
8.

Recent advances in protein-ligand interactions: molecular dynamics simulations and binding free energy.

Dubey KD, Tiwari RK, Ojha RP.

Curr Comput Aided Drug Des. 2013 Dec;9(4):518-31. Review.

PMID:
24138393
9.

Studying functional dynamics in bio-molecules using accelerated molecular dynamics.

Markwick PR, McCammon JA.

Phys Chem Chem Phys. 2011 Dec 7;13(45):20053-65. doi: 10.1039/c1cp22100k. Epub 2011 Oct 21. Review.

PMID:
22015376
10.

Molecular recognition of RNA: challenges for modelling interactions and plasticity.

Fulle S, Gohlke H.

J Mol Recognit. 2010 Mar-Apr;23(2):220-31. doi: 10.1002/jmr.1000. Review.

PMID:
19941322
11.

Estimation of conformational entropy in protein-ligand interactions: a computational perspective.

Polyansky AA, Zubac R, Zagrovic B.

Methods Mol Biol. 2012;819:327-53. doi: 10.1007/978-1-61779-465-0_21.

PMID:
22183546
12.

Modelling proteins: conformational sampling and reconstruction of folding kinetics.

Klenin K, Strodel B, Wales DJ, Wenzel W.

Biochim Biophys Acta. 2011 Aug;1814(8):977-1000. doi: 10.1016/j.bbapap.2010.09.006. Epub 2010 Sep 17. Review.

PMID:
20851219
13.

Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials.

Emperador A, Meyer T, Orozco M.

Proteins. 2010 Jan;78(1):83-94. doi: 10.1002/prot.22563.

PMID:
19816993
14.

Communication: Quantum polarized fluctuating charge model: a practical method to include ligand polarizability in biomolecular simulations.

Kimura SR, Rajamani R, Langley DR.

J Chem Phys. 2011 Dec 21;135(23):231101. doi: 10.1063/1.3671638.

PMID:
22191857
15.

Predicting protein ligand binding motions with the conformation explorer.

Flores SC, Gerstein MB.

BMC Bioinformatics. 2011 Oct 27;12:417. doi: 10.1186/1471-2105-12-417.

16.

Protein flexibility and ligand recognition: challenges for molecular modeling.

Spyrakis F, BidonChanal A, Barril X, Luque FJ.

Curr Top Med Chem. 2011;11(2):192-210. Review.

PMID:
20939788
17.

Headgroup conformations of phospholipids from molecular dynamics simulation: sampling challenges and comparison to experiment.

Vogel A, Feller SE.

J Membr Biol. 2012 Jan;245(1):23-8. doi: 10.1007/s00232-011-9411-5. Epub 2011 Dec 9.

PMID:
22159954
18.

Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins.

Ostermeir K, Zacharias M.

Biochim Biophys Acta. 2013 May;1834(5):847-53. doi: 10.1016/j.bbapap.2012.12.016. Epub 2013 Jan 5. Review.

PMID:
23298543
19.

Molecular dynamics simulations of the dimerization of transmembrane alpha-helices.

Psachoulia E, Marshall DP, Sansom MS.

Acc Chem Res. 2010 Mar 16;43(3):388-96. doi: 10.1021/ar900211k.

PMID:
20017540
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