Cited by ..

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 42 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

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