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Nucleic Acids Research 2006 34(Web Server issue):W128-W132; doi:10.1093/nar/gkl036
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

3dSS: 3D structural superposition

K. Sumathi1, P. Ananthalakshmi1, M. N. A. Md. Roshan1 and K. Sekar1,2,*

1 Bioinformatics Centre, Indian Institute of Science Bangalore 560 012, India 2 Supercomputer Education and Research Centre, Indian Institute of Science Bangalore 560 012, India

*To whom correspondence should be addressed. Tel: +91 080 23601409; Fax: +91 080 23600085; Email: sekar{at}physics.iisc.ernet.in, sekar{at}serc.iisc.ernet.in

Received October 6, 2005. Revised November 28, 2005. Accepted November 28, 2005.

3dSS is a web-based interactive computing server, primarily designed to aid researchers, to superpose two or several 3D protein structures. In addition, the server can be effectively used to find the invariant and common water molecules present in the superposed homologous protein structures. The molecular visualization tool RASMOL is interfaced with the server to visualize the superposed 3D structures with the water molecules (invariant or common) in the client machine. Furthermore, an option is provided to save the superposed 3D atomic coordinates in the client machine. To perform the above, users need to enter Protein Data Bank (PDB)-id(s) or upload the atomic coordinates in PDB format. This server uses a locally maintained PDB anonymous FTP server that is being updated weekly. This program can be accessed through our Bioinformatics web server at the URL http://cluster.physics.iisc.ernet.in/3dss/ or http://10.188.1.15/3dss/.

This work is dedicated to the late professor M. Sundaralingam

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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