DDI2PPI: An integrated web server for protein-protein interaction and residue contact matrix predictions Conference Paper
| Authors: | Du, T.; Gonzalez, A. J.; Wang, Q.; Huang, H.; Liao, L.; Wu, C. |
| Title: | DDI2PPI: An integrated web server for protein-protein interaction and residue contact matrix predictions |
| Conference Title: | 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics |
| Abstract: | Protein-protein interactions (PPIs) play essential roles in many biological processes. The large gap between the fast growing protein sequence information and the experimentally verified PPI information has motivated the development of computational methods to predict PPIs and residue-residue (RR) contacts. Although many tools are available for PPI predictions, most do not make a distinction between direct PPIs, which refer to physical contacts between two proteins, and indirect PPIs. Furthermore, few tools predict detailed RR contacts between interacting proteins, which are valuable for understanding chemical interaction mechanisms and designing investigations of the interaction. Here we present the web server DDI2PPI to provide PPI and RR contact matrix predictions from query protein sequences, focusing on predicting direct physical interactions. DDI2PPI implements algorithms that predict PPIs and RR contact matrices through domain-domain interaction (DDI) analysis based on interaction profile Hidden Markov Models (ipHMMs) and Support Vector Machines (SVMs). It covers more than 6000 DDI families in 3DID, a database of three-dimensional interacting domains. DDI2PPI (version 1.0) is freely available at http://annotation.dbi.udel.edu/ppifiprediction/. |
| Keywords: | proteins; prediction; artificial intelligence; forecasting; bioinformatics; drug interactions; support vector machines; biological process; world wide web; server; protein-protein interactions; machine learning; protein-protein interaction; learning systems; domain-domain interactions; web services; hidden markov models; physical interactions; markov processes; contact matrix; domain-domain interaction; residue- residue contact; query processing; servers; social networking (online); chemical interactions; interaction profiles; support vector machine (svms) |
| Journal Title | Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics |
| Conference Dates: | 2014 Sep 20-23 |
| Conference Location: | Newport Beach, CA |
| ISBN: | 978-1-4503-2894-4 |
| Publisher: | Assoc Computing Machinery |
| Date Published: | 2014-01-01 |
| Start Page: | 641 |
| End Page: | 642 |
| Language: | English |
| DOI: | 10.1145/2649387.2660814 |
| PROVIDER: | scopus |
| DOI/URL: | |
| Notes: | ACM BCB - ACM Conf. Bioinform., Comput. Biol., Health Informatics -- Conference code: 109745 -- Export Date: 2 February 2015 -- ACM Special Interest Group on Biomedical Computing (SIGBIO) -- 20 September 2014 through 23 September 2014 -- Source: Scopus |
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