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(PS)2: Protein Structure Prediction Server

(PS)2-v2 Server new

(PS)2 Server

Documentation

CASP6 predictions

Sample output

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 Documentation for (PS)2
  
 

Overview

        (PS)2 is an automated homology modeling server. The method uses an effective consensus strategy
by combining PSI-BLAST, IMPALA, and T-Coffee in both template selection and target-template alignment.
The final three dimensional structure is built using the modeling package MODELLER. After generated a 
predicted model with no other refinements, the program PROCHECK was used to evaluate the quality of 
this model based on the G-factor. Finally, the predicted model was displayed by Chime and automatically 
sent to users.



        Using (PS)2 is simple, just paste the sequence you want to query in the text area field on middle
of the page. You can then press the "SUBMIT" button to perform the query. The results will automatically
sent to users.

        The predicted model can also display by Chime. Chime plug-in for browsers should be installed.
You may download Chime from MDL Information System Inc.


Template(s) selection

  • Option "Both (PSI-BLAST & IMPALA)" will use the consensus of PSI-BLAST and IMPALA for the template search.
  • Option "PSI-BLAST" will use the PSI-BLAST only for the template search.
  • Option "IMPALA" will use the MPALA only for the template search.
  • Option "Use this PDB template" will use the specific PDB as the tempalete. PSI-BLAST PSI-BLAST is a method for detecting sequence homologs of a given protein. It uses the concept of searching with a position-specific residue substitution profile appropriate to the family in which the query belongs. This allows for more sensitive detection of remote homologous sequences. (PS)2 runs PSI-BLAST 2.2.6 locally.
  • Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29(14):2994-3005.
  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (17):3389-402 IMPALA IMPALA searches the query sequence against each of the template profiles, which constitute a database of PSI-BLAST-generated position-specific score matrices (PSSMs).
  • Schaffer AA, Wolf YI, Ponting CP, Koonin EV, Aravind L, Altschul SF. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics. 15, 1000-1011, 1999. T-Coffee T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment.
  • C.Notredame, D. Higgins, J. Heringa. T-Coffee: A novel method for multiple sequence alignments. J. Mol. Biol. 302, 205-217, 2000. Model building
  • Option "MODELLER" will use MODELLER for the model building.
  • Option "RAMP" will use RAMP for the model building. MODELLER MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms.
  • M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sanchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.
  • A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9, 1753-1773, 2000.
  • A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993. RAMP RAMP is a suite of programs to aid in the modelling of protein three-dimensional structure.
  • Hung L-H, Ngan S-C, Liu T, Samudrala R. PROTINFO: New algorithms for enhanced protein structure prediction. Nucleic Acids Research 33: W77-W80, 2005.
  • Hung L-H, Samudrala R. PROTINFO: Secondary and tertiary protein structure prediction. Nucleic Acids Research 31: 3296-3299, 2003.
  • Samudrala R, Levitt M. A comprehensive analysis of 40 blind protein structure predictions. BMC Structural Biology 2: 3-18, 2002. MODELLER licence key MODELLER is available free of charge for all academic non-profit institutions. Please read and accept the Academic License Agreement for MODELLER to receive a key Modeller Registration PROCHECK PROCHECK can check the stereochemical quality of a protein structure and the G-factor is the measurement.
  • Laskowski R A, MacArthur M W, Moss D S & Thornton J M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 26, 283-291, 1993. FASTA format description A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length. An example sequence in FASTA format is: >AAT03210 glyoxalase family protein MKIEHVALWTTNLEQMKQFYVTYFGATANDLYENKTKGFNSYFLSFEDGARLEIMSRTDV TGKTTGENLGWAHIAISTGTKEAVDELTEKLRQDGFAIAGEPRMTGDGYYESVVLDPEGN RIEITW Accepted amino acid codes are:
         A alanine     M methionine
         C cystine     N asparagine
         D aspartate     P proline
         E glutamate     Q glutamine
         F phenylalanine     R arginine
         G glycine     S serine
         H histidine     T threonine
         I isoleucine     V valine
         K lysine     W tryptophan
         L leucine     Y tyrosine
    Batch (by mail) A user will receive the final results by mail and our server will keep your predicted results one week.
  • Mail information:
  •    
    Job ID : 1107280034
    E-mail : chieh.bi91g@nctu.edu.tw

    (PS)2 results are available at http://ps2.life.nctu.edu.tw/temp/1107280034/
    The data will be kept at least 7 days after this message was send.
    Thanks for using (PS)2. Please send us comments to chieh.bi91g@nctu.edu.tw.
      
  • Final results: Final results consist of predicted structure, structure evaluation, selected templates, and alignments.
         You can view an example by clicking the following image.

         http://ps2.life.nctu.edu.tw/temp/1107280034/
  •  Final results
    Interactive User can change the selection of the templates and get the final results on the Web. When you enter the mail address, you can also receive the batch results by mail.
  • Template results: User can assign specific templates for the target from list of candidates. In the batch
         process, our (PS)2 will automaticlly assign the templates. This is the main difference between "Batch" mode
         and "Interactive" mode. You can view an example by clicking the following image.

  •    Template results
      
  • Final results: Final results consist of predicted structure, structure evaluation, selected templates, and alignments.
         You can view an example by clicking the following image.

  •  Final results
  •   
     
    Chen CC, Hwang JK, Yang JM. (PS)2: protein structure prediction server. NAR, 2006, Vol. 34, W152-W157