Protein Science
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

Protein Science (2007), 16:947-955. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
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 Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Zhou, H.
Right arrow Articles by Zhou, Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Zhou, H.
Right arrow Articles by Zhou, Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

DDOMAIN: Dividing structures into domains using a normalized domain–domain interaction profile

Hongyi Zhou1, Bin Xue1,2,3, and Yaoqi Zhou1,2,3

1 Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York 14214, USA
2 Indiana University School of Informatics, Indiana University-Purdue University, Indianapolis, Indiana 46202, USA
3 Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA

(RECEIVED October 2, 2006; FINAL REVISION February 7, 2007; ACCEPTED February 7, 2007)

Dividing protein structures into domains is proven useful for more accurate structural and functional characterization of proteins. Here, we develop a method, called DDOMAIN, that divides structure into DOMAINs using a normalized contact-based domain–domain interaction profile. Results of DDOMAIN are compared to AUTHORS annotations (domain definitions are given by the authors who solved protein structures), as well as to popular SCOP and CATH annotations by human experts and automatic programs. DDOMAIN's automatic annotations are most consistent with the AUTHORS annotations (90% agreement in number of domains and 88% agreement in both number of domains and at least 85% overlap in domain assignment of residues) if its three adjustable parameters are trained by the AUTHORS annotations. By comparison, the agreement is 83% (81% with at least 85% overlap criterion) between SCOP-trained DDOMAIN and SCOP annotations and 77% (73%) between CATH-trained DDOMAIN and CATH annotations. The agreement between DDOMAIN and AUTHORS annotations goes beyond single-domain proteins (97%, 82%, and 56% for single-, two-, and three-domain proteins, respectively). For an "easy" data set of proteins whose CATH and SCOP annotations agree with each other in number of domains, the agreement is 90% (89%) between "easy-set"-trained DDOMAIN and CATH/SCOP annotations. The consistency between SCOP-trained DDOMAIN and SCOP annotations is superior to two other recently developed, SCOP-trained, automatic methods PDP (protein domain parser), and DomainParser 2. We also tested a simple consensus method made of PDP, DomainParser 2, and DDOMAIN and a different version of DDOMAIN based on a more sophisticated statistical energy function. The DDOMAIN server and its executable are available in the services section on http://sparks.informatics.iupui.edu.

Keywords: structure/function studies; structural proteins; new methods; domain parser


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




HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 2007 by The Protein Society.