Nucleic Acids Research Advance Access originally published online on November 10, 2008
Nucleic Acids Research 2009 37(Database issue):D305-D309; doi:10.1093/nar/gkn869
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Nucleic Acids Research, 2009, Vol. 37, Database issue D305-D309
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse
1Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, 2Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610 and 3Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
*To whom correspondence should be addressed. Tel: +81 3 5978 5100; Fax: +81 3 3941 5990; Email: go.mitiko{at}ocha.ac.jp
Received August 11, 2008. Revised September 27, 2008. Accepted October 18, 2008.
We have constructed a database, AS-ALPS (alternative splicing-induced alteration of protein structure), which provides information that would be useful for analyzing the effects of alternative splicing (AS) on protein structure, interactions with other bio-molecules and protein interaction networks in human and mouse. Several AS events have been revealed to contribute to the diversification of protein structure, which results in diversification of interaction partners or affinities, which in turn contributes to regulation of bio-molecular networks. Most AS variants, however, are only known at the sequence level. It is important to determine the effects of AS on protein structure and interaction, and to provide candidates for experimental targets that are relevant to network regulation by AS. For this purpose, the three-dimensional (3D) structures of proteins are valuable sources of information; however, these have not been fully exploited in any other AS-related databases. AS-ALPS is the only AS-related database that describes the spatial relationships between protein regions altered by AS (‘AS regions’) and both the proteins’ hydrophobic cores and sites of inter-molecular interactions. This information makes it possible to infer whether protein structural stability and/or protein interaction are affected by each AS event. AS-ALPS can be freely accessed at http://as-alps.nagahama-i-bio.ac.jp and http://genomenetwork.nig.ac.jp/as-alps/.