Inferring protein domain interactions from databases of interacting proteins
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* Corresponding author: David Eisenberg david@mbi.ucla.edu
Genome Biology 2005, 6:R89 doi:10.1186/gb-2005-6-10-r89
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Research article
Yungki Park BMC Bioinformatics 2009, 10:419 (14 December 2009) |
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Methodology article
Kevin Y Yip, Philip M Kim, Drew McDermott, Mark Gerstein BMC Bioinformatics 2009, 10:241 (5 August 2009) The benefits of a multi-level machine-learning approach to predicting protein interactions are demonstrated by an algorithm that integrates predictions of interactions at the whole protein, domain and residue levels, improving the overall accuracy of predictions without propagating errors.
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Research article
Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder BMC Bioinformatics 2009, 10:196 (27 June 2009) |
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Review
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 Biology 2009, 10:207 (2 February 2009) This article is part of a collection on BioSapiens Where information on homologous proteins is available, progress is being made in automated prediction of protein function from sequence and structure. |
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Software
NetGrep: fast network schema searches in interactomes Eric Banks, Elena Nabieva, Ryan Peterson, Mona Singh Genome Biology 2008, 9:R138 (18 September 2008) NetGrep is a system for searching protein interaction networks for matches to user-supplied network schemas. |
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Research article
Interrogating domain-domain interactions with parsimony based approaches Katia S Guimarães, Teresa M Przytycka BMC Bioinformatics 2008, 9:171 (26 March 2008) |
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Research
The MoVIN server for the analysis of protein interaction networks Paolo Marcatili, Giovanni Bussotti, Anna Tramontano BMC Bioinformatics 2008, 9(Suppl 2):S11 (26 March 2008) |
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Research article
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 (16 October 2007) |
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Method
Haidong Wang, Eran Segal, Asa Ben-Hur, Qian-Ru Li, Marc Vidal, Daphne Koller Genome Biology 2007, 8:R192 (14 September 2007) InSite is a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs. |
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Research article
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 Pharmacology 2007, 7:10 (20 August 2007) |
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Research article
Reuse of structural domain–domain interactions in protein networks Benjamin Schuster-Böckler, Alex Bateman BMC Bioinformatics 2007, 8:259 (18 July 2007) |
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Methodology article
A domain-based approach to predict protein-protein interactions Mudita Singhal, Haluk Resat BMC Bioinformatics 2007, 8:199 (13 June 2007) |
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Research
Evolutionary conservation of domain-domain interactions Zohar Itzhaki, Eyal Akiva, Yael Altuvia, Hanah Margalit Genome Biology 2006, 7:R125 (21 December 2006) Mapping of domain-domain interactions onto the cellular protein-protein interaction networks of different organisms demonstrates that there is a catalogue of domain pairs that is used for mediating various interactions in the cell |
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Proceedings
An evaluation of human protein-protein interaction data in the public domain Suresh Mathivanan, Balamurugan Periaswamy, TKB Gandhi, Kumaran Kandasamy, Shubha Suresh, Riaz Mohmood, YL Ramachandra, Akhilesh Pandey BMC Bioinformatics 2006, 7(Suppl 5):S19 (18 December 2006) |
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Method
Predicting domain-domain interactions using a parsimony approach Katia S Guimarães, Raja Jothi, Elena Zotenko, Teresa M Przytycka Genome Biology 2006, 7:R104 (9 November 2006) A new parsimony approach for the prediction of domain-domain interactions is presented and demonstrated to provide improvement in prediction coverage and accuracy. |
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Research article
Stefan Wuchty BMC Genomics 2006, 7:122 (23 May 2006) |