NetCSSP

Net-CSSP
Neural networks for calculating Contact-dependent Secondary Structure Propensity
Applications in predicting non-native secondary structures and amyloid fibril formation


1. Select a method for CSSP calculation
Single network provides helical and beta propensity in a single profile while dual mode calculates the helical and
beta propensities in two separate neural networks.

single network dual networks


Three ways to submit a query sequence

2-1. Paste your protein sequence (Single letters) Display sample sequences

2-2. Type PDB ID to display CSSP profile with native secondary structure
 The sequence and structure information will be downloaded from RCSB Protein data bank
PDB ID (4 letters) :

(Ex. 3ERD)

2-3. Load a local PDB file from your computer


Search chameleon sequences
 - Compare native and non-native secondary structure propensities for a given sequence context
- Find fragments with high propensity for non-native secondary structures

 A total of 1,424,079 fragments with 7-residue length from 2,339 SCOP20 domains are in DB

Type sequence (Single letter) : (Up to 7 amino acids)
And / Or define CSSP threshold: >
See "Help" page for the explanation of threshold options.
 The threshold value for non-native P(helix) or non-native P(beta) is usually in the range of 0.1 - 0.5, while
 for relative P(helix) or relative P(beta), it is in the range of 1 - 5.

References
(Please cite the following papers when publishing your work using NetCSSP)


1. NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation. Changsik Kim,Jiwon Choi,
Seong Joon Lee, William J. Welsh and Sukjoon Yoon, Nucleic Acids Research (2009) 37: W469-73
2. CSSP2: an improved method for predicting contact-dependent secondary structure propensity. Sukjoon Yoon, William J. Welsh
and Heeyoung Jung. Computational Biology & Chemistry (2007) 31:373-377
3. Rapid assessment of contact-dependent secondary structure propensity: relevance to amyloidogenic sequences.Sukjoon Yoon,
William J. Welsh, Proteins (2005) 60:110-117
4. Detecting hidden sequence propensity for amyloid fibril formation.Sukjoon Yoon, William J. Welsh. Protein Science (2004) 13:
2149-2160



Last update: 6/22/2020 by Heeseung Yoo and Euna Jeong

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