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Nucleic Acids Research Advance Access originally published online on May 25, 2009
Nucleic Acids Research 2009 37(Web Server issue):W469-W473; doi:10.1093/nar/gkp351
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W469-W473
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation

Changsik Kim1, Jiwon Choi1, Seong Joon Lee1, William J. Welsh2 and Sukjoon Yoon1,*

1Sookmyung Women's University, Department of Biological Sciences, Hyochangwon-gil 52, Yongsan-gu, Seoul, Republic of Korea, 140-742 and 2University of Medicine & Dentistry of New Jersey (UMDNJ), Department of Pharmacology, Robert Wood Johnson Medical School and the Informatics Institute of UMDNJ, 675 Hoes Lane, Piscataway, NJ 08854, USA

*To whom correspondence should be addressed. Tel: +82 2 710 9415; Fax: +82 2 2077 7322; Email: yoonsj{at}sookmyung.ac.kr

Received January 22, 2009. Revised April 15, 2009. Accepted April 22, 2009.

The calculation of contact-dependent secondary structure propensity (CSSP) is a unique and sensitive method that detects non-native secondary structure propensities in protein sequences. This method has applications in predicting local conformational change, which typically is observed in core sequences of protein aggregation and amyloid fibril formation. NetCSSP implements the latest version of the CSSP algorithm and provides a Flash chart-based graphic interface that enables an interactive calculation of CSSP values for any user-selected regions in a given protein sequence. This feature also can quantitatively estimate the mutational effect on changes in native or non-native secondary structural propensities in local sequences. In addition, this web tool provides precalculated non-native secondary structure propensities for over 1 400 000 fragments that are seven-residues long, collected from PDB structures. They are searchable for chameleon subsequences that can serve as the core of amyloid fibril formation. The NetCSSP web tool is available at http://cssp2.sookmyung.ac.kr/.


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