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Items: 10


Functional modulation of a protein folding landscape via side-chain distortion.

Kelch BA, Salimi NL, Agard DA.

Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9414-9. doi: 10.1073/pnas.1119274109.


Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites.

Berkholz DS, Driggers CM, Shapovalov MV, Dunbrack RL Jr, Karplus PA.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):449-53. doi: 10.1073/pnas.1107115108.


Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone.

Dubay KH, Bothma JP, Geissler PL.

PLoS Comput Biol. 2011 Sep;7(9):e1002168. doi: 10.1371/journal.pcbi.1002168.


A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution.

Tronrud DE, Karplus PA.

Acta Crystallogr D Biol Crystallogr. 2011 Aug;67(Pt 8):699-706. doi: 10.1107/S090744491102292X.


Joint X-ray and neutron refinement with phenix.refine.

Afonine PV, Mustyakimov M, Grosse-Kunstleve RW, Moriarty NW, Langan P, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2010 Nov;66(Pt 11):1153-63. doi: 10.1107/S0907444910026582.


Conformation dependence of backbone geometry in proteins.

Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA.

Structure. 2009 Oct 14;17(10):1316-25. doi: 10.1016/j.str.2009.08.012.


Application of elastic network models to proteins in the crystalline state.

Riccardi D, Cui Q, Phillips GN Jr.

Biophys J. 2009 Jan;96(2):464-75. doi: 10.1016/j.bpj.2008.10.010. Erratum in: Biophys J. 2009 Mar 18;96(6):2548.


Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis.

Kong Y, Karplus M.

Proteins. 2009 Jan;74(1):145-54. doi: 10.1002/prot.22139.


The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models.

Sen TZ, Feng Y, Garcia JV, Kloczkowski A, Jernigan RL.

J Chem Theory Comput. 2006;2(3):696-704.


Do all backbone polar groups in proteins form hydrogen bonds?

Fleming PJ, Rose GD.

Protein Sci. 2005 Jul;14(7):1911-7. Review.

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