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Using Spectral Representation to Classify Proteins' Conformational States.

Saberi Fathi SM, Tuszynski JA.

Int J Mol Sci. 2018 Jul 18;19(7). pii: E2089. doi: 10.3390/ijms19072089.


Enhanced prediction of conformational flexibility and phosphorylation in proteins.

Swaminathan K, Adamczak R, Porollo A, Meller J.

Adv Exp Med Biol. 2010;680:307-19. doi: 10.1007/978-1-4419-5913-3_35.


A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T.

PLoS Comput Biol. 2009 May;5(5):e1000393. doi: 10.1371/journal.pcbi.1000393. Epub 2009 May 29.


Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions.

Yang LW, Eyal E, Chennubhotla C, Jee J, Gronenborn AM, Bahar I.

Structure. 2007 Jun;15(6):741-9.


Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces.

Bohnuud T, Kozakov D, Vajda S.

PLoS Comput Biol. 2014 Oct 2;10(10):e1003872. doi: 10.1371/journal.pcbi.1003872. eCollection 2014 Oct.


Analysis of cytochrome P450 CYP119 ligand-dependent conformational dynamics by two-dimensional NMR and X-ray crystallography.

Basudhar D, Madrona Y, Kandel S, Lampe JN, Nishida CR, de Montellano PR.

J Biol Chem. 2015 Apr 17;290(16):10000-17. doi: 10.1074/jbc.M114.627935. Epub 2015 Feb 10.


Towards a true protein movie: a perspective on the potential impact of the ensemble-based structure determination using exact NOEs.

Vögeli B, Orts J, Strotz D, Chi C, Minges M, Wälti MA, Güntert P, Riek R.

J Magn Reson. 2014 Apr;241:53-9. doi: 10.1016/j.jmr.2013.11.016. Review.


An integrative approach combining ion mobility mass spectrometry, X-ray crystallography, and nuclear magnetic resonance spectroscopy to study the conformational dynamics of α1 -antitrypsin upon ligand binding.

Nyon MP, Prentice T, Day J, Kirkpatrick J, Sivalingam GN, Levy G, Haq I, Irving JA, Lomas DA, Christodoulou J, Gooptu B, Thalassinos K.

Protein Sci. 2015 Aug;24(8):1301-12. doi: 10.1002/pro.2706. Epub 2015 Jul 14.


A community resource of experimental data for NMR / X-ray crystal structure pairs.

Everett JK, Tejero R, Murthy SB, Acton TB, Aramini JM, Baran MC, Benach J, Cort JR, Eletsky A, Forouhar F, Guan R, Kuzin AP, Lee HW, Liu G, Mani R, Mao B, Mills JL, Montelione AF, Pederson K, Powers R, Ramelot T, Rossi P, Seetharaman J, Snyder D, Swapna GV, Vorobiev SM, Wu Y, Xiao R, Yang Y, Arrowsmith CH, Hunt JF, Kennedy MA, Prestegard JH, Szyperski T, Tong L, Montelione GT.

Protein Sci. 2016 Jan;25(1):30-45. doi: 10.1002/pro.2774. Epub 2015 Sep 22. Review.


COCO: a simple tool to enrich the representation of conformational variability in NMR structures.

Laughton CA, Orozco M, Vranken W.

Proteins. 2009 Apr;75(1):206-16. doi: 10.1002/prot.22235.


Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering.

Venditti V, Egner TK, Clore GM.

Chem Rev. 2016 Jun 8;116(11):6305-22. doi: 10.1021/acs.chemrev.5b00592. Epub 2016 Jan 7. Review.


Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches.

Westenhoff S, Nazarenko E, Malmerberg E, Davidsson J, Katona G, Neutze R.

Acta Crystallogr A. 2010 Mar;66(Pt 2):207-19. doi: 10.1107/S0108767309054361. Epub 2010 Feb 18.


Assessing the chemical accuracy of protein structures via peptide acidity.

Anderson JS, Hernández G, LeMaster DM.

Biophys Chem. 2013 Jan;171:63-75. doi: 10.1016/j.bpc.2012.10.005. Epub 2012 Nov 2.


Solution NMR structure determination of proteins revisited.

Billeter M, Wagner G, Wüthrich K.

J Biomol NMR. 2008 Nov;42(3):155-8. doi: 10.1007/s10858-008-9277-8. Epub 2008 Oct 1. Review.


Performance of protein-ligand docking with simulated chemical shift perturbations.

Ten Brink T, Aguirre C, Exner TE, Krimm I.

J Chem Inf Model. 2015 Feb 23;55(2):275-83. doi: 10.1021/ci500446s. Epub 2014 Oct 30.


What can we learn by computing 13Calpha chemical shifts for X-ray protein models?

Arnautova YA, Vila JA, Martin OA, Scheraga HA.

Acta Crystallogr D Biol Crystallogr. 2009 Jul;65(Pt 7):697-703. doi: 10.1107/S0907444909012086. Epub 2009 Jun 20.


Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics.

Yang LW, Eyal E, Bahar I, Kitao A.

Bioinformatics. 2009 Mar 1;25(5):606-14. doi: 10.1093/bioinformatics/btp023. Epub 2009 Jan 15. Erratum in: Bioinformatics. 2009 Aug 15;25(16):2147.


Conformational distributions of unfolded polypeptides from novel NMR techniques.

Meier S, Blackledge M, Grzesiek S.

J Chem Phys. 2008 Feb 7;128(5):052204. doi: 10.1063/1.2838167.


Toward the quantum chemical calculation of nuclear magnetic resonance chemical shifts of proteins.

Frank A, Onila I, Möller HM, Exner TE.

Proteins. 2011 Jul;79(7):2189-202. doi: 10.1002/prot.23041. Epub 2011 May 9.


Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions.

Peng C, Zhang L, Head-Gordon T.

Biophys J. 2010 May 19;98(10):2356-64. doi: 10.1016/j.bpj.2010.01.044.

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