FlexPred: a web-server for predicting residue positions
involved in conformational switches in proteins


[HELP]

IMPORTANT: Please submit jobs with at least 3 second interval and do not submit more than 50 jobs at a time. Otherwise, the jobs will be deleted and your IP address blocked.

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Proteins are dynamic and flexible macromolecules. Upon changes in the environment, the protein backbone can undergo significant ordered conformational changes and switch from one folded conformation to another. This web-server predicts residue positions that may be involved in such ordered conformational switches. The prediction can be performed using either a user-supplied protein sequence or a protein structure in a Protein Data Bank (PDB) file. If a protein sequence is submitted, then the prediction is performed using sequence-derived information only (such as the profile of evolutionary conservation of residue positions). If a PDB file is submitted, then the prediction is performed using sequence-derived information and solvent accessibility of residue positions calculated from this file. Please note that this web-server is not meant to predict protein disorder (you may refer to DisProt for a list of disorder predictors). For more information on the methodology and accuracy of the prediction please refer to the original publication (Kuznetsov, 2008) and help link.


Step 1: Input options

Please select your input choice from the options given below.
(All amino acid sequences must be in FASTA format)

Enter a FASTA sequence

Paste your amino acid sequence in the box below:

Upload a FASTA sequence file


Upload a PDB file


Get a PDB file by ID



Step 2: Encoding of amino acid sequence

PSSM-based encoding (Recommended for sequence-based submissions)
Binary encoding (Recommended for PDB-based submissions)


Step 3: False Positive Rate (FPr)

Select desired FPr:


Step 4: Retrieval of the results

E-mail the results (Recommended). E-mail address:
Display a URL link to my process. I will check it manually.
(Data are kept on the web server for 24 hours, and deleted afterwards)

[Output format] [Expected wait time]

     

If you use this web-server, please cite the following articles:

Web-server citation: I.B.Kuznetsov and M.McDuffie, 2008, FlexPred: a web-server for predicting residue positions involved
in conformational switches in proteins. Bioinformation, 3(3):134-136

Methodology citation: I.B.Kuznetsov, 2008, Ordered conformational change in the protein backbone: prediction of
conformationally variable positions from sequence and low-resolution structural data.
Proteins: Structure, Function and Bioinformatics, 72(1):74-87

Please address your questions and comments to Igor Kuznetsov

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