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Items: 1 to 20 of 155

1.

Large-scale mapping of human protein interactome using structural complexes.

Tyagi M, Hashimoto K, Shoemaker BA, Wuchty S, Panchenko AR.

EMBO Rep. 2012 Mar 1;13(3):266-71. doi: 10.1038/embor.2011.261.

2.

Computational large-scale mapping of protein-protein interactions using structural complexes.

Shoemaker B, Wuchty S, Panchenko AR.

Curr Protoc Protein Sci. 2013 Sep 24;73:Unit 3.9. doi: 10.1002/0471140864.ps0309s73.

3.

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

Simonis N, Rual JF, Carvunis AR, Tasan M, Lemmens I, Hirozane-Kishikawa T, Hao T, Sahalie JM, Venkatesan K, Gebreab F, Cevik S, Klitgord N, Fan C, Braun P, Li N, Ayivi-Guedehoussou N, Dann E, Bertin N, Szeto D, Dricot A, Yildirim MA, Lin C, de Smet AS, Kao HL, Simon C, Smolyar A, Ahn JS, Tewari M, Boxem M, Milstein S, Yu H, Dreze M, Vandenhaute J, Gunsalus KC, Cusick ME, Hill DE, Tavernier J, Roth FP, Vidal M.

Nat Methods. 2009 Jan;6(1):47-54.

4.

Inferring physical protein contacts from large-scale purification data of protein complexes.

Schelhorn SE, Mestre J, Albrecht M, Zotenko E.

Mol Cell Proteomics. 2011 Jun;10(6):M110.004929. doi: 10.1074/mcp.M110.004929.

5.

Discover protein complexes in protein-protein interaction networks using parametric local modularity.

Kim J, Tan K.

BMC Bioinformatics. 2010 Oct 19;11:521. doi: 10.1186/1471-2105-11-521.

6.

Charting plant interactomes: possibilities and challenges.

Morsy M, Gouthu S, Orchard S, Thorneycroft D, Harper JF, Mittler R, Cushman JC.

Trends Plant Sci. 2008 Apr;13(4):183-91. doi: 10.1016/j.tplants.2008.01.006. Review.

PMID:
18329319
7.
8.

Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement.

Tuncbag N, Keskin O, Nussinov R, Gursoy A.

Proteins. 2012 Apr;80(4):1239-49. doi: 10.1002/prot.24022.

PMID:
22275112
9.
10.

Increasing confidence of protein interactomes using network topological metrics.

Chen J, Hsu W, Lee ML, Ng SK.

Bioinformatics. 2006 Aug 15;22(16):1998-2004.

PMID:
16787971
11.

Identifying the topology of protein complexes from affinity purification assays.

Friedel CC, Zimmer R.

Bioinformatics. 2009 Aug 15;25(16):2140-6. doi: 10.1093/bioinformatics/btp353.

12.

Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins.

Cho YR, Zhang A.

BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S3. doi: 10.1186/1471-2105-11-S3-S3.

13.

Interactome: gateway into systems biology.

Cusick ME, Klitgord N, Vidal M, Hill DE.

Hum Mol Genet. 2005 Oct 15;14 Spec No. 2:R171-81. Review.

PMID:
16162640
14.

An empirical framework for binary interactome mapping.

Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh KI, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, Cevik S, Simon C, de Smet AS, Dann E, Smolyar A, Vinayagam A, Yu H, Szeto D, Borick H, Dricot A, Klitgord N, Murray RR, Lin C, Lalowski M, Timm J, Rau K, Boone C, Braun P, Cusick ME, Roth FP, Hill DE, Tavernier J, Wanker EE, Barabási AL, Vidal M.

Nat Methods. 2009 Jan;6(1):83-90. doi: 10.1038/nmeth.1280.

15.

Analyzing protein-protein interaction networks.

Koh GC, Porras P, Aranda B, Hermjakob H, Orchard SE.

J Proteome Res. 2012 Apr 6;11(4):2014-31. doi: 10.1021/pr201211w. Review.

PMID:
22385417
16.

Pushing structural information into the yeast interactome by high-throughput protein docking experiments.

Mosca R, Pons C, Fernández-Recio J, Aloy P.

PLoS Comput Biol. 2009 Aug;5(8):e1000490. doi: 10.1371/journal.pcbi.1000490.

17.

Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces.

Burgoyne NJ, Jackson RM.

Bioinformatics. 2006 Jun 1;22(11):1335-42.

PMID:
16522669
18.

The Cartographers toolbox: building bigger and better human protein interaction networks.

Sanderson CM.

Brief Funct Genomic Proteomic. 2009 Jan;8(1):1-11. doi: 10.1093/bfgp/elp003. Review.

PMID:
19282470
19.

The protein interaction network mediated by human SH3 domains.

Carducci M, Perfetto L, Briganti L, Paoluzi S, Costa S, Zerweck J, Schutkowski M, Castagnoli L, Cesareni G.

Biotechnol Adv. 2012 Jan-Feb;30(1):4-15. doi: 10.1016/j.biotechadv.2011.06.012.

PMID:
21740962
20.

Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites.

Shoemaker BA, Zhang D, Thangudu RR, Tyagi M, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR.

Nucleic Acids Res. 2010 Jan;38(Database issue):D518-24. doi: 10.1093/nar/gkp842.

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