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: 2/01/2012
    Please send any comments or bug reports to Sukjoon Yoon