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Inferring protein domain interactions from databases of interacting proteins
Robert Riley, Christopher Lee, Chiara Sabatti, David Eisenberg
Genome Biol. 2005; 6(10): R89. Published online 2005 September 19. doi: 10.1186/gb-2005-6-10-r89
PMCID:
PMC1257472
Abstract Full Text PDF–611K Supplementary Material

Is Cited by the Following 44 Articles in this Archive:

Reduced Polymorphism in Domains Involved in Protein-Protein Interactions
Zohar Itzhaki, Hanah Margalit
PLoS One. 2012; 7(4): e34503. Published online 2012 April 3. doi: 10.1371/journal.pone.0034503
PMCID:
PMC3317993
Abstract Full Text PDF–453K Supplementary Material
Translating Mendelian and complex inheritance of Alzheimer's disease genes for predicting unique personal genome variants
Kelly Regan, Kanix Wang, Emily Doughty, Haiquan Li, Jianrong Li, Younghee Lee, Maricel G Kann, Yves A Lussier
J Am Med Inform Assoc. 2012 March; 19(2): 306–316. doi: 10.1136/amiajnl-2011-000656
PMCID:
PMC3277633
Abstract Full Text PDF–1.0M
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
Understanding and predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using domain genetic interactions
Bo Li, Weiguo Cao, Jizhong Zhou, Feng Luo
BMC Syst Biol. 2011; 5: 73. Published online 2011 May 17. doi: 10.1186/1752-0509-5-73
PMCID:
PMC3113237
Abstract Full Text PDF–489K 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
DIMA 3.0: Domain Interaction Map
Qibin Luo, Philipp Pagel, Baiba Vilne, Dmitrij Frishman
Nucleic Acids Res. 2011 January; 39(Database issue): D724–D729. Published online 2010 November 19. doi: 10.1093/nar/gkq1200
PMCID:
PMC3013740
Abstract Full Text PDF–1.1M
Algorithmic and analytical methods in network biology
Mehmet Koyutürk
Wiley Interdiscip Rev Syst Biol Med. Author manuscript; available in PMC 2011 May 4.
Published in final edited form as: Wiley Interdiscip Rev Syst Biol Med. 2010 MAY-JUN; 2(3): 277–292. doi: 10.1002/wsbm.61
PMCID:
PMC3087298
Abstract Full Text PDF–1.4M
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
Inferring protein function by domain context similarities in protein-protein interaction networks
Song Zhang, Hu Chen, Ke Liu, Zhirong Sun
BMC Bioinformatics. 2009; 10: 395. Published online 2009 December 2. doi: 10.1186/1471-2105-10-395
PMCID:
PMC2793267
Abstract Full Text PDF–334K
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
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels
Kevin Y Yip, Philip M Kim, Drew McDermott, Mark Gerstein
BMC Bioinformatics. 2009; 10: 241. Published online 2009 August 5. doi: 10.1186/1471-2105-10-241
PMCID:
PMC2734556
Abstract Full Text PDF–914K 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
Domain-oriented edge-based alignment of protein interaction networks
Xin Guo, Alexander J. Hartemink
Bioinformatics. 2009 June 15; 25(12): i240–1246. Published online 2009 May 27. doi: 10.1093/bioinformatics/btp202
PMCID:
PMC2687956
Abstract Full Text PDF–552K
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
Protein function annotation by homology-based inference
Yaniv Loewenstein, Domenico Raimondo, Oliver C Redfern, James Watson, Dmitrij Frishman, Michal Linial, Christine Orengo, Janet Thornton, Anna Tramontano
Genome Biol. 2009; 10(2): 207. Published online 2009 February 2. doi: 10.1186/gb-2009-10-2-207
PMCID:
PMC2688287
Abstract Full Text PDF–125K
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
Predicting and Validating Protein Interactions Using Network Structure
Pao-Yang Chen, Charlotte M. Deane, Gesine Reinert
PLoS Comput Biol. 2008 July; 4(7): e1000118. Published online 2008 July 25. doi: 10.1371/journal.pcbi.1000118
PMCID:
PMC2435280
Abstract Full Text PDF–277K 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
The MoVIN server for the analysis of protein interaction networks
Paolo Marcatili, Giovanni Bussotti, Anna Tramontano
BMC Bioinformatics. 2008; 9(Suppl 2): S11. Published online 2008 March 26. doi: 10.1186/1471-2105-9-S2-S11
PMCID:
PMC2323660
Abstract Full Text PDF–572K Supplementary Material
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
DIMA 2.0—predicted and known domain interactions
Philipp Pagel, Matthias Oesterheld, Oksana Tovstukhina, Norman Strack, Volker Stümpflen, Dmitrij Frishman
Nucleic Acids Res. 2008 January; 36(Database issue): D651–D655. Published online 2008 January. doi: 10.1093/nar/gkm996
PMCID:
PMC2238836
Abstract Full Text PDF–2.1M
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
The Modular Organization of Domain Structures: Insights into Protein–Protein Binding
Antonio del Sol, Pablo Carbonell
PLoS Comput Biol. 2007 December; 3(12): e239. Prepublished online 2007 October 18. Published online 2007 December 7. doi: 10.1371/journal.pcbi.0030239
PMCID:
PMC2134966
Abstract Full Text PDF–547K 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
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