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Results: 1 to 20 of 90

Similar articles for PubMed (Select 22084200)

1.

AH-DB: collecting protein structure pairs before and after binding.

Chang DT, Yao TJ, Fan CY, Chiang CY, Bai YH.

Nucleic Acids Res. 2012 Jan;40(Database issue):D472-8. doi: 10.1093/nar/gkr940. Epub 2011 Nov 13.

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3.

A quantitative measure of conformational changes in Apo, holo and ligand bound form of enzymes.

Singh S, Singh AK, Wadhwa G, Singh DB, Dwivedi S, Gautam B, Ramteke PW.

Interdiscip Sci. 2015 Apr 11. [Epub ahead of print]

PMID:
25863964
4.

Mathematical modeling of the apo and holo transcriptional regulation in Escherichia coli.

Alvarez-Vasquez FJ, Freyre-González JA, Balderas-Martínez YI, Delgado-Carrillo MI, Collado-Vides J.

Mol Biosyst. 2015 Apr;11(4):994-1003. doi: 10.1039/c4mb00561a.

PMID:
25683745
5.

Ensemble generation and the influence of protein flexibility on geometric tunnel prediction in cytochrome P450 enzymes.

Kingsley LJ, Lill MA.

PLoS One. 2014 Jun 23;9(6):e99408. doi: 10.1371/journal.pone.0099408. eCollection 2014.

6.

Protein function annotation by local binding site surface similarity.

Spitzer R, Cleves AE, Varela R, Jain AN.

Proteins. 2014 Apr;82(4):679-94. doi: 10.1002/prot.24450. Epub 2013 Nov 22.

7.

Real-time analysis and direct observations of different superoxide dismutase (SOD1) molecules bindings to aggregates in temporal evolution step.

Hong S, Lee S, Choi I, Yang YI, Kang T, Yi J.

Colloids Surf B Biointerfaces. 2013 Jan 1;101:266-71. doi: 10.1016/j.colsurfb.2012.06.014. Epub 2012 Jun 29.

PMID:
23010029
8.

DBD2BS: connecting a DNA-binding protein with its binding sites.

Chien TY, Lin CK, Lin CW, Weng YZ, Chen CY, Chang DT.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W173-9. doi: 10.1093/nar/gks564. Epub 2012 Jun 11.

9.

Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities.

Bianchi V, Gherardini PF, Helmer-Citterich M, Ausiello G.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S17. doi: 10.1186/1471-2105-13-S4-S17.

10.

On the applicability of elastic network normal modes in small-molecule docking.

Dietzen M, Zotenko E, Hildebrandt A, Lengauer T.

J Chem Inf Model. 2012 Mar 26;52(3):844-56. doi: 10.1021/ci2004847. Epub 2012 Feb 23. Erratum in: J Chem Inf Model. 2014 Dec 22;54(12):3453.

PMID:
22320151
11.

DOMMINO: a database of macromolecular interactions.

Kuang X, Han JG, Zhao N, Pang B, Shyu CR, Korkin D.

Nucleic Acids Res. 2012 Jan;40(Database issue):D501-6. doi: 10.1093/nar/gkr1128. Epub 2011 Dec 1.

12.

PoSSuM: a database of similar protein-ligand binding and putative pockets.

Ito J, Tabei Y, Shimizu K, Tsuda K, Tomii K.

Nucleic Acids Res. 2012 Jan;40(Database issue):D541-8. doi: 10.1093/nar/gkr1130. Epub 2011 Dec 1.

13.

Identification of key residues for protein conformational transition using elastic network model.

Su JG, Xu XJ, Li CH, Chen WZ, Wang CX.

J Chem Phys. 2011 Nov 7;135(17):174101. doi: 10.1063/1.3651480.

PMID:
22070286
14.

InterEvol database: exploring the structure and evolution of protein complex interfaces.

Faure G, Andreani J, Guerois R.

Nucleic Acids Res. 2012 Jan;40(Database issue):D847-56. doi: 10.1093/nar/gkr845. Epub 2011 Nov 3.

15.

Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis.

Wako H, Endo S.

Biophys Chem. 2011 Dec;159(2-3):257-66. doi: 10.1016/j.bpc.2011.07.004. Epub 2011 Jul 21.

PMID:
21807453
16.

Binding conformation prediction between human acetylcholinesterase and cytochrome c using molecular modeling methods.

Kim S, Lee Y, Lazar P, Son M, Baek A, Thangapandian S, Jeong NY, Yoo YH, Lee KW.

J Mol Graph Model. 2011 Aug;29(8):996-1005. doi: 10.1016/j.jmgm.2011.04.006. Epub 2011 Apr 27.

PMID:
21570330
17.

Structural instability and Cu-dependent pro-oxidant activity acquired by the apo form of mutant SOD1 associated with amyotrophic lateral sclerosis.

Kitamura F, Fujimaki N, Okita W, Hiramatsu H, Takeuchi H.

Biochemistry. 2011 May 24;50(20):4242-50. doi: 10.1021/bi200338h. Epub 2011 May 2.

PMID:
21506602
18.

An accurate feature-based method for identifying DNA-binding residues on protein surfaces.

Xiong Y, Liu J, Wei DQ.

Proteins. 2011 Feb;79(2):509-17. doi: 10.1002/prot.22898.

PMID:
21069866
19.

SAHG, a comprehensive database of predicted structures of all human proteins.

Motono C, Nakata J, Koike R, Shimizu K, Shirota M, Amemiya T, Tomii K, Nagano N, Sakaya N, Misoo K, Sato M, Kidera A, Hiroaki H, Shirai T, Kinoshita K, Noguchi T, Ota M.

Nucleic Acids Res. 2011 Jan;39(Database issue):D487-93. doi: 10.1093/nar/gkq1057. Epub 2010 Nov 3.

20.

Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies.

Kim DN, Altschuler J, Strong C, McGill G, Bathe M.

Nucleic Acids Res. 2011 Jan;39(Database issue):D451-5. doi: 10.1093/nar/gkq1088. Epub 2010 Nov 3.

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