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

Abstract

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/.