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Author, Editor

Author(s):

Zhu, Hongbo
Domingues, Francisco S.
Sommer, Ingolf
Lengauer, Thomas

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BibTeX cite key*:

Zhu2006

Title

Title*:

NOXclass: prediction of protein-protein interaction types

Journal

Journal Title*:

BMC Bioinformatics

Journal's URL:

http://www.biomedcentral.com/bmcbioinformatics

Download URL
for the article:

http://www.biomedcentral.com/content/pdf/1471-2105-7-27.pdf

Language:

English

Publisher

Publisher's
Name:

BioMed Central

Publisher's URL:

http://www.biomedcentral.com/home/

Publisher's
Address:

London, UK

ISSN:

14712105

Vol, No, Year, pp.

Volume:

7

Number:

27

Month:

January

Year*:

2006

Pages:

1-15

Number of VG Pages:

23

Sequence Number:

27

DOI:

10.1186/1471-2105-7-27

Abstract, Links, (C)

Note:


(LaTeX) Abstract:

Background
Structural models determined by X-ray crystallography play a central role in understanding protein-protein interactions at the molecular level. Interpretation of these models requires the distinction between non-specific crystal packing contacts and biologically relevant interactions. This has been investigated previously and classification approaches have been proposed. However, less attention has been devoted to distinguishing different types of biological interactions. These interactions are classified as obligate and non-obligate according to the effect of the complex formation on the stability of the protomers. So far no automatic classification methods for distinguishing obligate, non-obligate and crystal packing interactions have been made available.
Results
Six interface properties have been investigated on a dataset of 243 protein interactions. The six properties have been combined using a support vector machine algorithm, resulting in NOXclass, a classifier for distinguishing obligate, non-obligate and crystal packing interactions. We achieve an accuracy of 91.8% for the classification of these three types of interactions using a leave-one-out cross-validation procedure.
Conclusion
NOXclass allows the interpretation and analysis of protein quaternary structures. In particular, it generates testable hypotheses regarding the nature of protein-protein interactions, when experimental results are not available. We expect this server will benefit the users of protein structural models, as well as protein crystallographers and NMR spectroscopists. A web server based on the method and the datasets used in this study are available at http://noxclass.bioinf.mpi-inf.mpg.de/.

URL for the Abstract:

http://www.biomedcentral.com/1471-2105/7/27/abstract

Categories / Keywords:

Bioinformatics, Gene Ontology, Semantic Similarity, Functional Similarity

HyperLinks / References / URLs:


Copyright Message:

Copyright 2006 Schlicker et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Personal Comments:


Download
Access Level:

Public

Correlation

MPG Unit:

Max-Planck-Institut für Informatik



MPG Subunit:

Computational Biology and Applied Algorithmics

Audience:

popular

Appearance:

MPII WWW Server, MPII FTP Server, MPG publications list, university publications list, working group publication list, Fachbeirat, VG Wort



BibTeX Entry:

@MISC{Zhu2006,
AUTHOR = {Zhu, Hongbo and Domingues, Francisco S. and Sommer, Ingolf and Lengauer, Thomas},
TITLE = {{NOXclass}: prediction of protein-protein interaction types},
JOURNAL = {BMC Bioinformatics},
PUBLISHER = {BioMed Central},
YEAR = {2006},
NUMBER = {27},
VOLUME = {7},
PAGES = {1--15},
ADDRESS = {London, UK},
MONTH = {January},
ISBN = {14712105},
DOI = {10.1186/1471-2105-7-27},
}


Entry last modified by Hongbo Zhu, 12/18/2008
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Editor(s)
Andreas Schlicker
Created
02/22/2007 01:43:14 PM
Revisions
10.
9.
8.
7.
6.
Editor(s)
Hongbo Zhu
Hongbo Zhu
Hongbo Zhu
Ingolf Sommer
Ingolf Sommer
Edit Dates
18/12/2008 17:48:19
18/12/2008 17:47:21
05/03/2007 05:17:29 PM
03/20/2007 04:47:57 PM
26.02.2007 16:08:19
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