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

被引：70
作者：
Kim, Changsik [1 ]
Choi, Jiwon [1 ]
Lee, Seong Joon [1 ]
Welsh, William J. [2 ,3 ]
Yoon, Sukjoon [1 ]
机构：
[1] Sookmyung Womens Univ, Dept Biol Sci, Seoul 140742, South Korea
[2] Univ Med & Dent New Jersey, Robert Wood Johnson Med Sch, Dept Pharmacol, Piscataway, NJ 08854 USA
[3] Univ Med & Dent New Jersey, Inst Informat, Piscataway, NJ 08854 USA
来源：
NUCLEIC ACIDS RESEARCH | 2009年 / 37卷
关键词：
SECONDARY STRUCTURE PROPENSITY; AGGREGATION RATES; NEURAL NETWORKS; PROTEIN; SEGMENTS;
D O I：
10.1093/nar/gkp351
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
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 nonnative 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/.
引用
收藏
页码：W469 / W473
页数：5
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