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Results: 1 to 20 of 148

1.

New space warping method for the simulation of large-scale macromolecular conformational changes.

Jaqaman K, Ortoleva PJ.

J Comput Chem. 2002 Mar;23(4):484-91.

PMID:
11908085
[PubMed - indexed for MEDLINE]
2.
3.

Computer simulations of macromolecular dynamics: models for vibrational spectroscopy and X-ray refinement.

Levy RM.

Ann N Y Acad Sci. 1986;482:24-43.

PMID:
3471107
[PubMed - indexed for MEDLINE]
4.

Metadynamics in essential coordinates: free energy simulation of conformational changes.

Spiwok V, Lipovová P, Králová B.

J Phys Chem B. 2007 Mar 29;111(12):3073-6. Epub 2007 Mar 6.

PMID:
17388445
[PubMed - indexed for MEDLINE]
5.

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.

Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC.

J Chem Phys. 2007 Apr 21;126(15):155101.

PMID:
17461665
[PubMed - indexed for MEDLINE]
6.
7.

Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides.

Ishitani R, Shimizu K, Terada T.

J Chem Phys. 2006 Jun 7;124(21):214902.

PMID:
16774437
[PubMed - indexed for MEDLINE]
8.

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]
9.

Bayesian inference applied to macromolecular structure determination.

Habeck M, Nilges M, Rieping W.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Sep;72(3 Pt 1):031912. Epub 2005 Sep 20.

PMID:
16241487
[PubMed - indexed for MEDLINE]
10.

Normal mode analysis using the driven molecular dynamics method. II. An application to biological macromolecules.

Kaledin M, Brown A, Kaledin AL, Bowman JM.

J Chem Phys. 2004 Sep 22;121(12):5646-53.

PMID:
15366988
[PubMed - indexed for MEDLINE]
11.

Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

Noé F, Horenko I, Schütte C, Smith JC.

J Chem Phys. 2007 Apr 21;126(15):155102.

PMID:
17461666
[PubMed - indexed for MEDLINE]
12.

Protein conformational landscapes: energy minimization and clustering of a long molecular dynamics trajectory.

Troyer JM, Cohen FE.

Proteins. 1995 Sep;23(1):97-110.

PMID:
8539254
[PubMed - indexed for MEDLINE]
13.

Geometry optimization of molecular clusters and complexes using scaled internal coordinates.

Maslen PE.

J Chem Phys. 2005 Jan 1;122(1):14104.

PMID:
15638639
[PubMed - indexed for MEDLINE]
14.

Sampling small-scale and large-scale conformational changes in proteins and molecular complexes.

Yun MR, Mousseau N, Derreumaux P.

J Chem Phys. 2007 Mar 14;126(10):105101.

PMID:
17362087
[PubMed - indexed for MEDLINE]
15.

Overcoming entropic barrier with coupled sampling at dual resolutions.

Lwin TZ, Luo R.

J Chem Phys. 2005 Nov 15;123(19):194904.

PMID:
16321110
[PubMed - indexed for MEDLINE]
16.

Using free energy perturbation to predict effects of changing force field parameters on computed conformational equilibriums of peptides.

Cao Z, Liu H.

J Chem Phys. 2008 Jul 7;129(1):015101. doi: 10.1063/1.2944248.

PMID:
18624500
[PubMed - indexed for MEDLINE]
17.

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.

Hamelberg D, Mongan J, McCammon JA.

J Chem Phys. 2004 Jun 22;120(24):11919-29.

PMID:
15268227
[PubMed - indexed for MEDLINE]
18.

Two-center-multipole expansion method: application to macromolecular systems.

Solov'yov IA, Yakubovich AV, Solov'yov AV, Greiner W.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 May;75(5 Pt 1):051912. Epub 2007 May 17.

PMID:
17677103
[PubMed - indexed for MEDLINE]
19.

An efficient molecular docking using conformational space annealing.

Lee K, Czaplewski C, Kim SY, Lee J.

J Comput Chem. 2005 Jan 15;26(1):78-87.

PMID:
15538770
[PubMed - indexed for MEDLINE]

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