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InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale
Haidong Wang, Eran Segal, Asa Ben-Hur, Qian-Ru Li, Marc Vidal, Daphne Koller
Genome Biol. 2007; 8(9): R192. Published online 2007 September 14. doi: 10.1186/gb-2007-8-9-r192
PMCID:
PMC2375030
Abstract Full Text PDF–947K Supplementary Material
 Is Cited by the Following 15 Articles in this Archive:
Fumonisin and Ochratoxin Production in Industrial Aspergillus niger Strains
Jens C. Frisvad, Thomas O. Larsen, Ulf Thrane, Martin Meijer, Janos Varga, Robert A. Samson, Kristian F. Nielsen
PLoS One. 2011; 6(8): e23496. Published online 2011 August 11. doi: 10.1371/journal.pone.0023496
PMCID:
PMC3154942
Abstract Full Text PDF–97K Supplementary Material
Binding Site Prediction for Protein-Protein Interactions and Novel Motif Discovery using Re-occurring Polypeptide Sequences
Adam Amos-Binks, Catalin Patulea, Sylvain Pitre, Andrew Schoenrock, Yuan Gui, James R Green, Ashkan Golshani, Frank Dehne
BMC Bioinformatics. 2011; 12: 225. Published online 2011 June 2. doi: 10.1186/1471-2105-12-225
PMCID:
PMC3120708
Abstract Full Text PDF–989K Supplementary Material
DOMINE: a comprehensive collection of known and predicted domain-domain interactions
Sailu Yellaboina, Asba Tasneem, Dmitri V. Zaykin, Balaji Raghavachari, Raja Jothi
Nucleic Acids Res. 2011 January; 39(Database issue): D730–D735. Published online 2010 November 27. doi: 10.1093/nar/gkq1229
PMCID:
PMC3013741
Abstract Full Text PDF–4.1M
Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction
Aalt D. J. van Dijk, Giuseppa Morabito, Martijn Fiers, Roeland C. H. J. van Ham, Gerco C. Angenent, Richard G. H. Immink
PLoS Comput Biol. 2010 November; 6(11): e1001017. Published online 2010 November 24. doi: 10.1371/journal.pcbi.1001017
PMCID:
PMC2991254
Abstract Full Text PDF–817K Supplementary Material
Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins
Yanjun Qi, Oznur Tastan, Jaime G. Carbonell, Judith Klein-Seetharaman, Jason Weston
Bioinformatics. 2010 September 15; 26(18): i645–i652. Published online 2010 September 4. doi: 10.1093/bioinformatics/btq394
PMCID:
PMC2935441
Abstract Full Text PDF–295K
Struct2Net: a web service to predict protein–protein interactions using a structure-based approach
Rohit Singh, Daniel Park, Jinbo Xu, Raghavendra Hosur, Bonnie Berger
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W508–W515. Published online 2010 May 29. doi: 10.1093/nar/gkq481
PMCID:
PMC2896152
Abstract Full Text PDF–4.6M
Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences
Yungki Park
BMC Bioinformatics. 2009; 10: 419. Published online 2009 December 14. doi: 10.1186/1471-2105-10-419
PMCID:
PMC2803199
Abstract Full Text PDF–511K Supplementary Material
Knowledge-guided inference of domain–domain interactions from incomplete protein–protein interaction networks
Mei Liu, Xue-wen Chen, Raja Jothi
Bioinformatics. 2009 October 1; 25(19): 2492–2499. Published online 2009 August 10. doi: 10.1093/bioinformatics/btp480
PMCID:
PMC2752622
Abstract Full Text PDF–458K Supplementary Material
A Complex-based Reconstruction of the Saccharomyces cerevisiae Interactome
Haidong Wang, Boyko Kakaradov, Sean R. Collins, Lena Karotki, Dorothea Fiedler, Michael Shales, Kevan M. Shokat, Tobias C. Walther, Nevan J. Krogan, Daphne Koller
Mol Cell Proteomics. 2009 June; 8(6): 1361–1381. doi: 10.1074/mcp.M800490-MCP200
PMCID:
PMC2690481
Abstract Full Text
ModLink+: improving fold recognition by using protein–protein interactions
Oriol Fornes, Ramon Aragues, Jordi Espadaler, Marc A. Marti-Renom, Andrej Sali, Baldo Oliva
Bioinformatics. 2009 June 15; 25(12): 1506–1512. Published online 2009 April 8. doi: 10.1093/bioinformatics/btp238
PMCID:
PMC2687990
Abstract Full Text PDF–609K
A protein domain-based interactome network for C. elegans early embryogenesis
Mike Boxem, Zoltan Maliga, Niels Klitgord, Na Li, Irma Lemmens, Miyeko Mana, Lorenzo de Lichtervelde, Joram D. Mul, Diederik van de Peut, Maxime Devos, Nicolas Simonis, Muhammed A. Yildirim, Murat Cokol, Huey-Ling Kao, Anne-Sophie de Smet, Haidong Wang, Anne-Lore Schlaitz, Tong Hao, Stuart Milstein, Changyu Fan, Mike Tipsword, Kevin Drew, Matilde Galli, Kahn Rhrissorrakrai, David Drechsel, Daphne Koller, Frederick P. Roth, Lilia M. Iakoucheva, A. Keith Dunker, Richard Bonneau, Kristin C. Gunsalus, David E. Hill, Fabio Piano, Jan Tavernier, Sander van den Heuvel, Anthony A. Hyman, Marc Vidal
Cell. Author manuscript; available in PMC 2009 August 8.
Published in final edited form as: Cell. 2008 August 8; 134(3): 534–545. doi: 10.1016/j.cell.2008.07.009
PMCID:
PMC2596478
Abstract Full Text PDF–4.0M Supplementary Material
Global investigation of protein–protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences
S. Pitre, C. North, M. Alamgir, M. Jessulat, A. Chan, X. Luo, J. R. Green, M. Dumontier, F. Dehne, A. Golshani
Nucleic Acids Res. 2008 August; 36(13): 4286–4294. Published online 2008 August. doi: 10.1093/nar/gkn390
PMCID:
PMC2490765
Abstract Full Text PDF–312K Supplementary Material
An en masse phenotype and function prediction system for Mus musculus
Murat Taşan, Weidong Tian, David P Hill, Francis D Gibbons, Judith A Blake, Frederick P Roth
Genome Biol. 2008; 9(Suppl 1): S8. Published online 2008 June 27. doi: 10.1186/gb-2008-9-s1-s8
PMCID:
PMC2447542
Abstract Full Text PDF–2.8M Supplementary Material
Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein–protein interaction dataset
Jie Guo, Xiaomei Wu, Da-Yong Zhang, Kui Lin
Nucleic Acids Res. 2008 April; 36(6): 2002–2011. Published online 2008 April. doi: 10.1093/nar/gkn016
PMCID:
PMC2346601
Abstract Full Text PDF–423K
Interrogating domain-domain interactions with parsimony based approaches
Katia S Guimarães, Teresa M Przytycka
BMC Bioinformatics. 2008; 9: 171. Published online 2008 March 26. doi: 10.1186/1471-2105-9-171
PMCID:
PMC2358894
Abstract Full Text PDF–1.1M Supplementary Material
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