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Predicting domain-domain interactions using a parsimony approach
Katia S Guimarães, Raja Jothi, Elena Zotenko, Teresa M Przytycka
Genome Biol. 2006; 7(11): R104. Published online 2006 November 9. doi: 10.1186/gb-2006-7-11-r104
PMCID:
PMC1794579
Abstract Full Text PDF–475K Supplementary Material
 Is Cited by the Following 26 Articles in this Archive:
Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes
Amin R. Mazloom, Ruth Dannenfelser, Neil R. Clark, Arsen V. Grigoryan, Kathryn M. Linder, Timothy J. Cardozo, Julia C. Bond, Aislyn D. W. Boran, Ravi Iyengar, Anna Malovannaya, Rainer B. Lanz, Avi Ma'ayan
PLoS Comput Biol. 2011 December; 7(12): e1002319. Published online 2011 December 29. doi: 10.1371/journal.pcbi.1002319
PMCID:
PMC3248428
Abstract Full Text PDF–2.4M 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
Using context to improve protein domain identification
Alejandro Ochoa, Manuel Llinás, Mona Singh
BMC Bioinformatics. 2011; 12: 90. Published online 2011 March 31. doi: 10.1186/1471-2105-12-90
PMCID:
PMC3090354
Abstract Full Text PDF–1.3M Supplementary Material
The role of exon shuffling in shaping protein-protein interaction networks
Douglas V Cancherini, Gustavo S França, Sandro J de Souza
BMC Genomics. 2010; 11(Suppl 5): S11. Published online 2010 December 22. doi: 10.1186/1471-2164-11-S5-S11
PMCID:
PMC3045794
Abstract Full Text PDF–460K 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
Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines
Alvaro J González, Li Liao
BMC Bioinformatics. 2010; 11: 537. Published online 2010 October 29. doi: 10.1186/1471-2105-11-537
PMCID:
PMC2989984
Abstract Full Text PDF–1.1M
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions
Yosuke Ozawa, Rintaro Saito, Shigeo Fujimori, Hisashi Kashima, Masamichi Ishizaka, Hiroshi Yanagawa, Etsuko Miyamoto-Sato, Masaru Tomita
BMC Bioinformatics. 2010; 11: 350. Published online 2010 June 28. doi: 10.1186/1471-2105-11-350
PMCID:
PMC2905371
Abstract Full Text PDF–790K Supplementary Material
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
DASMIweb: online integration, analysis and assessment of distributed protein interaction data
Hagen Blankenburg, Fidel Ramírez, Joachim Büch, Mario Albrecht
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W122–W128. Published online 2009 July 1. doi: 10.1093/nar/gkp438
PMCID:
PMC2703953
Abstract Full Text PDF–2.6M
Triangle network motifs predict complexes by complementing high-error interactomes with structural information
Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder
BMC Bioinformatics. 2009; 10: 196. Published online 2009 June 27. doi: 10.1186/1471-2105-10-196
PMCID:
PMC2714575
Abstract Full Text PDF–3.0M Supplementary Material
Proteome-wide Prediction of Signal Flow Direction in Protein Interaction Networks Based on Interacting Domains
Wei Liu, Dong Li, Jian Wang, Hongwei Xie, Yunping Zhu, Fuchu He
Mol Cell Proteomics. 2009 September; 8(9): 2063–2070. Published online 2009 June 5. doi: 10.1074/mcp.M800354-MCP200
PMCID:
PMC2742434
Abstract Full Text Supplementary Material
DASMI: exchanging, annotating and assessing molecular interaction data
Hagen Blankenburg, Robert D. Finn, Andreas Prlić, Andrew M. Jenkinson, Fidel Ramírez, Dorothea Emig, Sven-Eric Schelhorn, Joachim Büch, Thomas Lengauer, Mario Albrecht
Bioinformatics. 2009 May 15; 25(10): 1321–1328. Published online 2009 May 5. doi: 10.1093/bioinformatics/btp142
PMCID:
PMC2677739
Abstract Full Text PDF–496K Supplementary Material
A Top-Down Approach to Infer and Compare Domain-Domain Interactions across Eight Model Organisms
Chittibabu Guda, Brian R. King, Lipika R. Pal, Purnima Guda
PLoS ONE. 2009; 4(3): e5096. Published online 2009 March 31. doi: 10.1371/journal.pone.0005096
PMCID:
PMC2659750
Abstract Full Text PDF–533K Supplementary Material
Organization of Physical Interactomes as Uncovered by Network Schemas
Eric Banks, Elena Nabieva, Bernard Chazelle, Mona Singh
PLoS Comput Biol. 2008 October; 4(10): e1000203. Published online 2008 October 24. doi: 10.1371/journal.pcbi.1000203
PMCID:
PMC2561054
Abstract Full Text PDF–1.2M Supplementary Material
NetGrep: fast network schema searches in interactomes
Eric Banks, Elena Nabieva, Ryan Peterson, Mona Singh
Genome Biol. 2008; 9(9): R138. Published online 2008 September 18. doi: 10.1186/gb-2008-9-9-r138
PMCID:
PMC2592716
Abstract Full Text PDF–1.8M Supplementary Material
Unraveling Protein Networks with Power Graph Analysis
Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder
PLoS Comput Biol. 2008 July; 4(7): e1000108. Published online 2008 July 11. doi: 10.1371/journal.pcbi.1000108
PMCID:
PMC2424176
Abstract Full Text PDF–2.4M
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
Protein Interaction Predictions from Diverse Sources
Yin Liu, Inyoung Kim, Hongyu Zhao
Drug Discov Today. Author manuscript; available in PMC 2011 August 30.
Published in final edited form as: Drug Discov Today. 2008 May; 13(9-10): 409–416. Published online 2008 March 6. doi: 10.1016/j.drudis.2008.01.005
PMCID:
PMC3164358
Abstract Full Text PDF–423K
DOMINE: a database of protein domain interactions
Balaji Raghavachari, Asba Tasneem, Teresa M. Przytycka, Raja Jothi
Nucleic Acids Res. 2008 January; 36(Database issue): D656–D661. Published online 2008 January. doi: 10.1093/nar/gkm761
PMCID:
PMC2238965
Abstract Full Text PDF–378K Supplementary Material
Analysis on multi-domain cooperation for predicting protein-protein interactions
Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen
BMC Bioinformatics. 2007; 8: 391. Published online 2007 October 16. doi: 10.1186/1471-2105-8-391
PMCID:
PMC2222654
Abstract Full Text PDF–3.4M Supplementary Material
Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
Doron Betel, Kevin E Breitkreuz, Ruth Isserlin, Danielle Dewar-Darch, Mike Tyers, Christopher W. V Hogue
PLoS Comput Biol. 2007 September; 3(9): e182. Published online 2007 September 21. doi: 10.1371/journal.pcbi.0030182
PMCID:
PMC1988853
Abstract Full Text PDF–364K Supplementary Material
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
An integrative in silico approach for discovering candidates for drug-targetable protein-protein interactions in interactome data
Nobuyoshi Sugaya, Kazuyoshi Ikeda, Toshiyuki Tashiro, Shizu Takeda, Jun Otomo, Yoshiko Ishida, Akiko Shiratori, Atsushi Toyoda, Hideki Noguchi, Tadayuki Takeda, Satoru Kuhara, Yoshiyuki Sakaki, Takao Iwayanagi
BMC Pharmacol. 2007; 7: 10. Published online 2007 August 20. doi: 10.1186/1471-2210-7-10
PMCID:
PMC2045083
Abstract Full Text PDF–1.0M Supplementary Material
A domain-based approach to predict protein-protein interactions
Mudita Singhal, Haluk Resat
BMC Bioinformatics. 2007; 8: 199. Published online 2007 June 13. doi: 10.1186/1471-2105-8-199
PMCID:
PMC1919395
Abstract Full Text PDF–1.7M Supplementary Material
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