Skip Navigation

Nucleic Acids Research 2004 32(Web Server Issue):W569-W571; doi:10.1093/nar/gkh481
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (100K) 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 Liu, J.
Right arrow Articles by Rost, B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Liu, J.
Right arrow Articles by Rost, B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

CHOP: parsing proteins into structural domains

Jinfeng Liu1,2,4 and Burkhard Rost1,2,3,*

1 CUBIC and 2 North East Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA, 3 Columbia University Center for Computational Biology and Bioinformatics (C2B2), Russ Berrie Pavilion, 1150 Saint Nicholas Avenue, New York, NY 10032, USA and 4 Department of Pharmacology, Columbia University, 630 West 168th Street, New York, NY 10032, USA

* To whom correspondence should be addressed at Department of Biochemistry and Molecular Biophysics, Columbia University, 650 W 168th Street, BB-217, New York, NY 10032, USA. Tel: +1 212 305 4018; Fax: +1 212 305 7932; Email: rost{at}columbia.edu

Received February 14, 2004; Revised April 16, 2004; Accepted May 4, 2004

Sequence-based domain assignment is one of the most important and challenging problems in structural biology. We have developed a method, CHOP, that chops proteins into domain-like fragments. The basic idea is to cut proteins from entirely sequenced organisms beginning from very reliable experimental information (Protein Data Bank), proceeding to expert annotations of domain-like regions (Pfam-A) and completing through cuts based on termini of native protein ends. The CHOP server takes protein sequences as input and returns the dissections supported by homology transfer. CHOP results are precompiled for many entirely sequenced proteomes. The service is available at http://www.rostlab.org/services/CHOP/.

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 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.


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
 Nucleic Acids ResHome page
G. Pugalenthi, G. Archunan, and R. Sowdhamini
DIAL: a web-based server for the automatic identification of structural domains in proteins
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W130 - W132.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Mika and B. Rost
NMPdb: Database of Nuclear Matrix Proteins
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D160 - D163.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Liu and B. Rost
Sequence-based prediction of protein domains
Nucleic Acids Res., July 7, 2004; 32(12): 3522 - 3530.
[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.