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Items: 1 to 20 of 133

1.

Elastic network models capture the motions apparent within ensembles of RNA structures.

Zimmermann MT, Jernigan RL.

RNA. 2014 Jun;20(6):792-804. doi: 10.1261/rna.041269.113. Epub 2014 Apr 23.

2.

MAVENs: motion analysis and visualization of elastic networks and structural ensembles.

Zimmermann MT, Kloczkowski A, Jernigan RL.

BMC Bioinformatics. 2011 Jun 28;12:264. doi: 10.1186/1471-2105-12-264.

3.

Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion.

Stember JN, Wriggers W.

J Chem Phys. 2009 Aug 21;131(7):074112. doi: 10.1063/1.3167410.

4.

Comparison of mode analyses at different resolutions applied to nucleic acid systems.

Van Wynsberghe AW, Cui Q.

Biophys J. 2005 Nov;89(5):2939-49. Epub 2005 Aug 12.

5.

Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models.

Zhang Z, Pfaendtner J, Grafm├╝ller A, Voth GA.

Biophys J. 2009 Oct 21;97(8):2327-37. doi: 10.1016/j.bpj.2009.08.007.

6.

Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model.

Kurkcuoglu O, Turgut OT, Cansu S, Jernigan RL, Doruker P.

Biophys J. 2009 Aug 19;97(4):1178-87. doi: 10.1016/j.bpj.2009.06.009.

7.

Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes.

Yang L, Song G, Carriquiry A, Jernigan RL.

Structure. 2008 Feb;16(2):321-30. doi: 10.1016/j.str.2007.12.011.

8.

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.

9.

Domain decomposition-based structural condensation of large protein structures for understanding their conformational dynamics.

Kim JI, Na S, Eom K.

J Comput Chem. 2011 Jan 15;32(1):161-9. doi: 10.1002/jcc.21613.

PMID:
20645300
10.

Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.

Pinamonti G, Bottaro S, Micheletti C, Bussi G.

Nucleic Acids Res. 2015 Sep 3;43(15):7260-9. doi: 10.1093/nar/gkv708. Epub 2015 Jul 17.

11.

The use of experimental structures to model protein dynamics.

Katebi AR, Sankar K, Jia K, Jernigan RL.

Methods Mol Biol. 2015;1215:213-36. doi: 10.1007/978-1-4939-1465-4_10.

12.

Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses.

Ahmed A, Villinger S, Gohlke H.

Proteins. 2010 Dec;78(16):3341-52. doi: 10.1002/prot.22841.

PMID:
20848551
13.

Dynamics of large proteins through hierarchical levels of coarse-grained structures.

Doruker P, Jernigan RL, Bahar I.

J Comput Chem. 2002 Jan 15;23(1):119-27.

PMID:
11913377
14.

Packing regularities in biological structures relate to their dynamics.

Jernigan RL, Kloczkowski A.

Methods Mol Biol. 2007;350:251-76.

15.

Global ribosome motions revealed with elastic network model.

Wang Y, Rader AJ, Bahar I, Jernigan RL.

J Struct Biol. 2004 Sep;147(3):302-14.

PMID:
15450299
16.

Global motions of the nuclear pore complex: insights from elastic network models.

Lezon TR, Sali A, Bahar I.

PLoS Comput Biol. 2009 Sep;5(9):e1000496. doi: 10.1371/journal.pcbi.1000496. Epub 2009 Sep 4.

17.

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.

18.
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20.

Efficient prediction of protein conformational pathways based on the hybrid elastic network model.

Seo S, Jang Y, Qian P, Liu WK, Choi JB, Lim BS, Kim MK.

J Mol Graph Model. 2014 Feb;47:25-36. doi: 10.1016/j.jmgm.2013.10.009. Epub 2013 Nov 1.

PMID:
24296313

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