TIM-Finder: A TIM-barrel Fold Recognition System |
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About TIM-Finder
TIM-Finder has been developed to predict whether a protein belongs to the TIM-barrel fold. With the assistance of Support Vector Machine(SVM)(http://www.csie.ntu.edu.tw/~cjlin/), TIM-Finder combined three different descriptors which are the sequence-alignment-based descriptor using PSI-BLAST e-values and bit scores, the descriptor based on the secondary structure element alignment (SSEA), and the descriptor based on the occurrence of PROSITE functional motifs. Given a query sequence, TIM-Finder scans a database of TIM-barrel proteins, calculates the scores based on the established SVM models, and produces a list of potential homologs. Based on the SCOP database (version 1.73), the current TIM-Finder library contains 322 TIM-barrel proteins, in which the sequence identity for any sequence pair is less than 40%. Usage The input is the sequence with FASTA format, and the email address is required since the result will be sent to it. A session ID will be generated when you submit a sequence, and you can query the result through this ID when the processing is ready. The result page consists of the SCOP IDs, SCOP classes, scores, PDB links and sequence links of the generated hits. Datasets and source code Available under request from Jingna Si . Reference Jing-Na Si, Ren-Xiang Yan, Chuan Wang, Ziding Zhang, and Xiao-Dong Su. TIM-Finder: A novel method to recognize TIM-barrel proteins. BMC structural Biology 2009, 9:73 Copyright This server is free available to any user, but without any warranty.
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©
Ziding Zhang's Laboratory
of Protein Bioinformatics 04 / 2009 |