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Nucleic Acids Research Advance Access originally published online on May 6, 2009
Nucleic Acids Research 2009 37(Web Server issue):W545-W551; doi:10.1093/nar/gkp291
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W545-W551
© 2009 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.

Articles

iSARST: an integrated SARST web server for rapid protein structural similarity searches

Wei-Cheng Lo1, Che-Yu Lee1, Chi-Ching Lee1,2 and Ping-Chiang Lyu1,3,*

1Institute of Bioinformatics and Structural Biology, 2Institute of Information System Application and 3Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan

*To whom correspondence should be addressed. Tel: +886 3 5742762; Fax: +886 3 5715934; Email: lslpc{at}life.nthu.edu.tw

Received February 22, 2009. Revised April 14, 2009. Accepted April 14, 2009.

iSARST is a web server for efficient protein structural similarity searches. It is a multi-processor, batch-processing and integrated implementation of several structural comparison tools and two database searching methods: SARST for common structural homologs and CPSARST for homologs with circular permutations. iSARST allows users submitting multiple PDB/SCOP entry IDs or an archive file containing many structures. After scanning the target database using SARST/CPSARST, the ordering of hits are refined with conventional structure alignment tools such as FAST, TM-align and SAMO, which are run in a PC cluster. In this way, iSARST achieves a high running speed while preserving the high precision of refinement engines. The final outputs include tables listing co-linear or circularly permuted homologs of the query proteins and a functional summary of the best hits. Superimposed structures can be examined through an interactive and informative visualization tool. iSARST provides the first batch mode structural comparison web service for both co-linear homologs and circular permutants. It can serve as a rapid annotation system for functionally unknown or hypothetical proteins, which are increasing rapidly in this post-genomics era. The server can be accessed at http://sarst.life.nthu.edu.tw/iSARST/.


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