Skip Navigation

Nucleic Acids Research 2006 34(Web Server issue):W128-W132; doi:10.1093/nar/gkl036
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (3531K) Freely available
Right arrow Screen PDF (464K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Sumathi, K.
Right arrow Articles by Sekar, K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Sumathi, K.
Right arrow Articles by Sekar, K.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Biol. Chem.Home page
C. Rodriguez-Almazan, R. Arreola, D. Rodriguez-Larrea, B. Aguirre-Lopez, M. T. de Gomez-Puyou, R. Perez-Montfort, M. Costas, A. Gomez-Puyou, and A. Torres-Larios
Structural Basis of Human Triosephosphate Isomerase Deficiency: MUTATION E104D IS RELATED TO ALTERATIONS OF A CONSERVED WATER NETWORK AT THE DIMER INTERFACE
J. Biol. Chem., August 22, 2008; 283(34): 23254 - 23263.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.