PubMed

A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectories.

Yang H, Parthasarathy S, Ucar D.

Algorithms Mol Biol. 2007 Apr 4;2:3.PMID: 17407611 [PubMed]Free PMC ArticleFree textRelated citations

A wavelet approach for the analysis of folding trajectory of protein Trp-cage.

Ye L, Chen H, Liu T, Wu Z, Li J, Zhou R.

J Bioinform Comput Biol. 2005 Dec;3(6):1351-70.PMID: 16374911 [PubMed - indexed for MEDLINE]Related citations

An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories.

Sun H, Ferhatosmanoglu H, Ota M, Wang Y.

BMC Bioinformatics. 2008 Aug 18;9:344.PMID: 18710565 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Towards data warehousing and mining of protein unfolding simulation data.

Berrar D, Stahl F, Silva C, Rodrigues JR, Brito RM, Dubitzky W.

J Clin Monit Comput. 2005 Oct;19(4-5):307-17.PMID: 16328945 [PubMed - indexed for MEDLINE]Related citations

Enhanced partial order curve comparison over multiple protein folding trajectories.

Sun H, Ferhatosmanoglu H, Ota M, Wang Y.

Comput Syst Bioinformatics Conf. 2007;6:299-310.PMID: 17951833 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Combinatorial pattern discovery approach for the folding trajectory analysis of a beta-hairpin.

Parida L, Zhou R.

PLoS Comput Biol. 2005 Jun;1(1):e8. Epub 2005 Jun 24.PMID: 16103909 [PubMed]Free PMC ArticleFree textRelated citations

PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory.

Zhou R, Parida L, Kapila K, Mudur S.

Bioinformatics. 2007 Jan 1;23(1):99-106. Epub 2006 Oct 24.PMID: 17062588 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Analysis of the free-energy surface of proteins from reversible folding simulations.

Allen LR, Krivov SV, Paci E.

PLoS Comput Biol. 2009 Jul;5(7):e1000428. Epub 2009 Jul 10.PMID: 19593364 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Structural search and retrieval using a tableau representation of protein folding patterns.

Konagurthu AS, Stuckey PJ, Lesk AM.

Bioinformatics. 2008 Mar 1;24(5):645-51. Epub 2008 Jan 5.PMID: 18175768 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Probing invisible, low-populated States of protein molecules by relaxation dispersion NMR spectroscopy: an application to protein folding.

Korzhnev DM, Kay LE.

Acc Chem Res. 2008 Mar;41(3):442-51. Epub 2008 Feb 15. Review.PMID: 18275162 [PubMed - indexed for MEDLINE]Related citations

Predicting the folding pathway of engrailed homeodomain with a probabilistic roadmap enhanced reaction-path algorithm.

Li DW, Yang H, Han L, Huo S.

Biophys J. 2008 Mar 1;94(5):1622-9. Epub 2007 Nov 16.PMID: 18024496 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Understanding the role of the topology in protein folding by computational inverse folding experiments.

Mucherino A, Costantini S, di Serafino D, D'Apuzzo M, Facchiano A, Colonna G.

Comput Biol Chem. 2008 Aug;32(4):233-9. Epub 2008 Apr 8.PMID: 18479970 [PubMed - indexed for MEDLINE]Related citations

From helix-coil transitions to protein folding.

Scheraga HA.

Biopolymers. 2008 May;89(5):479-85.PMID: 18008324 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Single-molecule fluorescence studies of protein folding.

Nienhaus GU.

Methods Mol Biol. 2009;490:311-37.PMID: 19157089 [PubMed - indexed for MEDLINE]Related citations

Study of early events in the protein folding of villin headpiece using molecular dynamics simulation.

Sonavane UB, Ramadugu SK, Joshi RR.

J Biomol Struct Dyn. 2008 Oct;26(2):203-14.PMID: 18597542 [PubMed - indexed for MEDLINE]Related citations

Study of multiple unfolding trajectories and unfolded states of the protein GB1 under the physical property space.

Wang J, Zhao L, Dou X, Zhang Z.

J Biomol Struct Dyn. 2008 Jun;25(6):609-19.PMID: 18399694 [PubMed - indexed for MEDLINE]Related citations

Identification of the protein folding transition state from molecular dynamics trajectories.

Muff S, Caflisch A.

J Chem Phys. 2009 Mar 28;130(12):125104.PMID: 19334897 [PubMed - indexed for MEDLINE]Related citations

Asymmetric kinetics of protein structural changes.

Marchal S, Font J, Ribó M, Vilanova M, Phillips RS, Lange R, Torrent J.

Acc Chem Res. 2009 Jun 16;42(6):778-87.PMID: 19378977 [PubMed - indexed for MEDLINE]Related citations

Understanding protein folding: small proteins in silico.

Zimmermann O, Hansmann UH.

Biochim Biophys Acta. 2008 Jan;1784(1):252-8. Epub 2007 Nov 6. Review.PMID: 18036571 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Protein folding simulations: from coarse-grained model to all-atom model.

Zhang J, Li W, Wang J, Qin M, Wu L, Yan Z, Xu W, Zuo G, Wang W.

IUBMB Life. 2009 Jun;61(6):627-43. Review.PMID: 19472192 [PubMed - indexed for MEDLINE]Related citations