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Results: 1 to 20 of 120

1.

Generalized spring tensor models for protein fluctuation dynamics and conformation changes.

Na H, Lin TL, Song G.

Adv Exp Med Biol. 2014;805:107-35. doi: 10.1007/978-3-319-02970-2_5.

PMID:
24446359
[PubMed - indexed for MEDLINE]
2.

Generalized spring tensor models for protein fluctuation dynamics and conformation changes.

Lin TL, Song G.

BMC Struct Biol. 2010 May 17;10 Suppl 1:S3. doi: 10.1186/1472-6807-10-S1-S3.

PMID:
20487510
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

A unification of the elastic network model and the Gaussian network model for optimal description of protein conformational motions and fluctuations.

Zheng W.

Biophys J. 2008 May 15;94(10):3853-7. doi: 10.1529/biophysj.107.125831. Epub 2008 Jan 30.

PMID:
18234807
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Tensorial elastic network model for protein dynamics: integration of the anisotropic network model with bond-bending and twist elasticities.

Srivastava A, Halevi RB, Veksler A, Granek R.

Proteins. 2012 Dec;80(12):2692-700. doi: 10.1002/prot.24153. Epub 2012 Aug 21.

PMID:
22847894
[PubMed - indexed for MEDLINE]
5.

Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor.

Doruker P, Atilgan AR, Bahar I.

Proteins. 2000 Aug 15;40(3):512-24.

PMID:
10861943
[PubMed - indexed for MEDLINE]
6.

A natural unification of GNM and ANM and the role of inter-residue forces.

Na H, Song G.

Phys Biol. 2014 Jun;11(3):036002. doi: 10.1088/1478-3975/11/3/036002. Epub 2014 Apr 15.

PMID:
24732806
[PubMed - in process]
7.

The gaussian network model: precise prediction of residue fluctuations and application to binding problems.

Erman B.

Biophys J. 2006 Nov 15;91(10):3589-99. Epub 2006 Aug 25.

PMID:
16935951
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models.

Eyal E, Chennubhotla C, Yang LW, Bahar I.

Bioinformatics. 2007 Jul 1;23(13):i175-84.

PMID:
17646294
[PubMed - indexed for MEDLINE]
Free Article
9.

Identification of motions in membrane proteins by elastic network models and their experimental validation.

Isin B, Tirupula KC, Oltvai ZN, Klein-Seetharaman J, Bahar I.

Methods Mol Biol. 2012;914:285-317. doi: 10.1007/978-1-62703-023-6_17.

PMID:
22976035
[PubMed - indexed for MEDLINE]
10.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug 2;10(4):040301. [Epub ahead of print]

PMID:
23912807
[PubMed - as supplied by publisher]
11.

Models with energy penalty on interresidue rotation address insufficiencies of conventional elastic network models.

Yang LW.

Biophys J. 2011 Apr 6;100(7):1784-93. doi: 10.1016/j.bpj.2011.02.033.

PMID:
21463592
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

vGNM: a better model for understanding the dynamics of proteins in crystals.

Song G, Jernigan RL.

J Mol Biol. 2007 Jun 8;369(3):880-93. Epub 2007 Mar 28.

PMID:
17451743
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Elastic network normal modes provide a basis for protein structure refinement.

Gniewek P, Kolinski A, Jernigan RL, Kloczkowski A.

J Chem Phys. 2012 May 21;136(19):195101. doi: 10.1063/1.4710986.

PMID:
22612113
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Coarse grained normal mode analysis vs. refined Gaussian Network Model for protein residue-level structural fluctuations.

Park JK, Jernigan R, Wu Z.

Bull Math Biol. 2013 Jan;75(1):124-60. doi: 10.1007/s11538-012-9797-y. Epub 2013 Jan 8.

PMID:
23296997
[PubMed - indexed for MEDLINE]
15.

Distance matrix-based approach to protein structure prediction.

Kloczkowski A, Jernigan RL, Wu Z, Song G, Yang L, Kolinski A, Pokarowski P.

J Struct Funct Genomics. 2009 Mar;10(1):67-81. doi: 10.1007/s10969-009-9062-2. Epub 2009 Feb 18.

PMID:
19224393
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Coarse-grained modeling of the actin filament derived from atomistic-scale simulations.

Chu JW, Voth GA.

Biophys J. 2006 Mar 1;90(5):1572-82. Epub 2005 Dec 16.

PMID:
16361345
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone.

Murarka RK, Liwo A, Scheraga HA.

J Chem Phys. 2007 Oct 21;127(15):155103.

PMID:
17949219
[PubMed - indexed for MEDLINE]
18.

Analysis of Conformational Motions and Residue Fluctuations for Escherichia coli Ribose-Binding Protein Revealed with Elastic Network Models.

Li HY, Cao ZX, Zhao LL, Wang JH.

Int J Mol Sci. 2013 May 21;14(5):10552-69. doi: 10.3390/ijms140510552.

PMID:
23698778
[PubMed]
Free PMC Article
19.

A large-scale comparison of computational models on the residue flexibility for NMR-derived proteins.

Zhang H, Shi H, Hanlon M.

Protein Pept Lett. 2012 Feb;19(2):244-51.

PMID:
21933137
[PubMed - indexed for MEDLINE]
20.

Anharmonic normal mode analysis of elastic network model improves the modeling of atomic fluctuations in protein crystal structures.

Zheng W.

Biophys J. 2010 Jun 16;98(12):3025-34. doi: 10.1016/j.bpj.2010.03.027.

PMID:
20550915
[PubMed - indexed for MEDLINE]
Free PMC Article

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