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Results: 1 to 20 of 91

1.

A high-performance parallel-generalized Born implementation enabled by tabulated interaction rescaling.

Larsson P, Lindahl E.

J Comput Chem. 2010 Nov 15;31(14):2593-600. doi: 10.1002/jcc.21552.

PMID:
20740558
[PubMed - indexed for MEDLINE]
2.

Treecode-based generalized Born method.

Xu Z, Cheng X, Yang H.

J Chem Phys. 2011 Feb 14;134(6):064107. doi: 10.1063/1.3552945.

PMID:
21322661
[PubMed - indexed for MEDLINE]
3.

Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.

Hassan SA, Mehler EL, Zhang D, Weinstein H.

Proteins. 2003 Apr 1;51(1):109-25.

PMID:
12596268
[PubMed - indexed for MEDLINE]
4.

An efficient hybrid explicit/implicit solvent method for biomolecular simulations.

Lee MS, Salsbury FR Jr, Olson MA.

J Comput Chem. 2004 Dec;25(16):1967-78.

PMID:
15470756
[PubMed]
5.

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born.

Götz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker RC.

J Chem Theory Comput. 2012 May 8;8(5):1542-1555. Epub 2012 Mar 26.

PMID:
22582031
[PubMed]
Free PMC Article
6.

Parallel Generalized Born Implicit Solvent Calculations with NAMD.

Tanner DE, Chan KY, Phillips JC, Schulten K.

J Chem Theory Comput. 2011 Nov 8;7(11):3635-3642.

PMID:
22121340
[PubMed]
Free PMC Article
7.

Free energy landscape of protein folding in water: explicit vs. implicit solvent.

Zhou R.

Proteins. 2003 Nov 1;53(2):148-61.

PMID:
14517967
[PubMed - indexed for MEDLINE]
8.

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

Gallicchio E, Levy RM.

J Comput Chem. 2004 Mar;25(4):479-99.

PMID:
14735568
[PubMed - indexed for MEDLINE]
9.

ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model.

Vorobjev YN, Hermans J.

Biophys Chem. 1999 Apr 5;78(1-2):195-205.

PMID:
10343388
[PubMed - indexed for MEDLINE]
10.

Simulation of peptide folding with explicit water--a mean solvation method.

Wu XW, Sung SS.

Proteins. 1999 Feb 15;34(3):295-302.

PMID:
10024017
[PubMed - indexed for MEDLINE]
11.

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation.

Roe DR, Okur A, Wickstrom L, Hornak V, Simmerling C.

J Phys Chem B. 2007 Feb 22;111(7):1846-57. Epub 2007 Jan 27.

PMID:
17256983
[PubMed - indexed for MEDLINE]
13.

A new strategy of exploring metabolomics data using Monte Carlo tree.

Cao DS, Wang B, Zeng MM, Liang YZ, Xu QS, Zhang LX, Li HD, Hu QN.

Analyst. 2011 Mar 7;136(5):947-54. doi: 10.1039/c0an00383b. Epub 2010 Dec 15.

PMID:
21157593
[PubMed - indexed for MEDLINE]
14.

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
[PubMed - indexed for MEDLINE]
15.

Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.

Simonson T, Carlsson J, Case DA.

J Am Chem Soc. 2004 Apr 7;126(13):4167-80.

PMID:
15053606
[PubMed - indexed for MEDLINE]
16.

An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme.

Arnold GE, Ornstein RL.

Proteins. 1994 Jan;18(1):19-33.

PMID:
8146120
[PubMed - indexed for MEDLINE]
17.

Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models.

Shen My MY, Freed KF.

Biophys J. 2002 Apr;82(4):1791-808.

PMID:
11916839
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function.

Taylor RD, Jewsbury PJ, Essex JW.

J Comput Chem. 2003 Oct;24(13):1637-56.

PMID:
12926007
[PubMed - indexed for MEDLINE]
19.

A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes.

Tanizaki S, Feig M.

J Chem Phys. 2005 Mar 22;122(12):124706.

PMID:
15836408
[PubMed - indexed for MEDLINE]
20.

Comparative study of generalized born models: Born radii and peptide folding.

Zhu J, Alexov E, Honig B.

J Phys Chem B. 2005 Feb 24;109(7):3008-22.

PMID:
16851315
[PubMed - indexed for MEDLINE]

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