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Items: 1 to 20 of 128

1.

Application of replica exchange umbrella sampling to protein structure refinement of nontemplate models.

Olson MA, Lee MS.

J Comput Chem. 2013 Jul 30;34(20):1785-93. doi: 10.1002/jcc.23325. Epub 2013 May 23.

PMID:
23703032
2.

Structure refinement of protein model decoys requires accurate side-chain placement.

Olson MA, Lee MS.

Proteins. 2013 Mar;81(3):469-78. doi: 10.1002/prot.24204. Epub 2012 Nov 12.

PMID:
23070940
3.

Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations.

Olson MA, Chaudhury S, Lee MS.

J Comput Chem. 2011 Nov 15;32(14):3014-22. doi: 10.1002/jcc.21883. Epub 2011 Jul 25.

PMID:
21793008
4.

Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement.

Olson MA, Lee MS.

PLoS One. 2014 May 21;9(5):e96638. doi: 10.1371/journal.pone.0096638. eCollection 2014 May 21.

5.

Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models.

Yeh IC, Lee MS, Olson MA.

J Phys Chem B. 2008 Nov 27;112(47):15064-73. doi: 10.1021/jp802469g.

PMID:
18959439
6.

Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent.

Kannan S, Zacharias M.

Proteins. 2010 Oct;78(13):2809-19. doi: 10.1002/prot.22796.

PMID:
20635348
7.

Can molecular dynamics simulations provide high-resolution refinement of protein structure?

Chen J, Brooks CL 3rd.

Proteins. 2007 Jun 1;67(4):922-30.

PMID:
17373704
8.

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.

Olson MA, Feig M, Brooks CL 3rd.

J Comput Chem. 2008 Apr 15;29(5):820-31.

PMID:
17876760
9.

Refinement of NMR structures using implicit solvent and advanced sampling techniques.

Chen J, Im W, Brooks CL 3rd.

J Am Chem Soc. 2004 Dec 15;126(49):16038-47.

PMID:
15584737
10.

Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models.

Fan H, Periole X, Mark AE.

Proteins. 2012 Jul;80(7):1744-54. doi: 10.1002/prot.24068. Epub 2012 Apr 13.

PMID:
22411697
13.

How well can we predict native contacts in proteins based on decoy structures and their energies?

Zhu J, Zhu Q, Shi Y, Liu H.

Proteins. 2003 Sep 1;52(4):598-608.

PMID:
12910459
14.

Simulated annealing coupled replica exchange molecular dynamics--an efficient conformational sampling method.

Kannan S, Zacharias M.

J Struct Biol. 2009 Jun;166(3):288-94. doi: 10.1016/j.jsb.2009.02.015. Epub 2009 Mar 9.

PMID:
19272454
16.

Assessment of Detection and Refinement Strategies for de novo Protein Structures Using Force Field and Statistical Potentials.

Lee MS, Olson MA.

J Chem Theory Comput. 2007 Jan;3(1):312-24. doi: 10.1021/ct600195f.

PMID:
26627174
17.

Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.

Raval A, Piana S, Eastwood MP, Dror RO, Shaw DE.

Proteins. 2012 Aug;80(8):2071-9. doi: 10.1002/prot.24098. Epub 2012 May 15.

PMID:
22513870
18.

Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles.

Ostermeir K, Zacharias M.

J Comput Chem. 2014 Jan 15;35(2):150-8. doi: 10.1002/jcc.23476. Epub 2013 Oct 31.

PMID:
24318649
19.

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.

Mishra SK, Kara M, Zacharias M, Koca J.

Glycobiology. 2014 Jan;24(1):70-84. doi: 10.1093/glycob/cwt093. Epub 2013 Oct 16.

PMID:
24134878
20.

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

Ostermeir K, Zacharias M.

Proteins. 2014 Dec;82(12):3410-9. doi: 10.1002/prot.24695. Epub 2014 Oct 10.

PMID:
25243707

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