VALPRED 3D

Please provide a PDB file. Upload the PDB file from your computer.
Please note that this PDB file is not validated, so make sure that it is a valid PDB file.

or
Enter the PDB file contents here.
Please note that these PDB file contents are not validated, so make sure that they are valid PDB file contents.
(Provide either a file or enter the contents here, not both.
If both provided, then contents here will be processed instead of uploaded file.)

Please note that if your PDB file is too big for this server (ie. more than approx. 250 residues), this server will not give an answer and will either display a blank page or time out. To know what can be done if this happens, please see the explanations below left.

OPTIONS :

SASA RESOLUTION : 
(Solvent Assessible Surface Area)
IGNORE HETATOMS : 
GRAPH RESIDUE WIDTH : 
GRAPH HEIGHT : 
DISPLAY OPTIONS :
Profiles 3D :  Show line:
Line colour:
Line label:
Smooth line:
REPIMPS :  Show line:
Line colour:
Line label:
Smooth line:

Notes about running this web page :

If your PDB file has too many residues in it for this server (ie. more than approx. 250 residues), this web page will time out and not display the result (it will display a blank page, or take a long time to process and then eventually time out.).

In that case, you can either download this Perl program from http://www.canoz.com/valpred/valpred3d_pl.txt
and run it on your own cgi-script perl-enabled web server, or run it in command line mode in your own Perl installation, (Linux Ubuntu 8.04 was used for testing).

Your own web server may allow the program to run for longer before timing out.

In command line mode, depending on your computer's memory size, you will probably be able to process longer sequences (our Linux testing machine was able to process 1800 residue long sequences).

You can also download the Windows version of this program from http://www.canoz.com/valpred/valpred_execution_files_jun2009.zip or from http://www.canoz.com/valpred/valpred_execution_files_jun2009.rar and run it on your Windows PC (Windows XP Home Edition was used for testing).

When you need to process sequences that are too long for the machine you are using, then a valid strategy is to break up your sequence into overlapping pieces, run each separately, and visually piece them together.




References :

Lawrence K. Lee, Noeris K. Salam, Hong Wing Lee, Emma M. Rath and W. Bret Church (in preparation)
'Transmembrane helix analysis using threading approaches'

James U. Bowie, Roland Lüthy, David Eisenberg (1991)
'A Method to Identify Protein Sequences that Fold into a Known Three-Dimensional Structure'
Science, 253, 164-170

Roland Lüthy, James U. Bowie, David Eisenberg (1992)
'Assessment of protein models with three-dimensional profiles'
Nature, 356, 83-85

Siavoush Dastmalchi, Michael B. Morris and W. Bret Church (2001)
'Modelling of the structural features of integral-membrane proteins using REPIMPS
(Reverse-Environment Prediction of Integral Membrane Protein Structure)'
Protein Science, 10, 1529-1538


Benchmarking :

This VALPRED program, including both its VALPRED1 and VALPRED2 algorithms,
have been benchmarked at the Benchmark of Membrane Helix Predictions from Sequence server.


Source Code : valpred3d_pl.txt



COPYRIGHT :
Valpred Windows Program Copyright © 2010 Lawrence K. Lee. All rights reserved.
Valpred Perl Program Copyright © 2010 Emma M. Rath. All rights reserved.
Soon this program will be released under an open source software license such as GNU General Public License or
Creative Commons license for Free Software Foundation's GNU General Public License at creativecommons.org