VALPRED 2D

Enter an amino acid sequence in FASTA format.
Then press the GO button to predict transmembrane segments (TMS)
using the VALPRED algorithm, which uses the PROFILES3D and REPIMPS
algorithms of solvent-accessible surface area.


eg. Enter the FASTA sequence as :

>1h2s_B Sensory rhodopsin II
AVFIFVGALTVLFGAIAYGEVTAAAATGDAAAVQEAAVSA
ILGLIILLGINLGLVAATL

or as :

AVFIFVGALTVLFGAIAYGEVTAAAATGDAAAVQEAAVSA
ILGLIILLGINLGLVAATL

Here is an example output graph from VALPRED :
output from VALPRED

Here is an example output graph from VALPRED2 :
output from VALPRED2

Here is another example of input :

>KCSA_STRLI Voltage-gated potassium channel
MPPMLSGLLARLVKLLLGRHGSALHWRAAGAATVLLVIVL
LAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGD
LYPVTLWGRLVAVVVMVAGITSFGLVTAALATWFVGREQE
RRGHFVRHSEKAAEEAYTRTTRALHERFDRLERMLDDNRR


Notes about running this web page :

If your amino acid sequence is too long for this server (around over 600 residues long), 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/perl_valpred_2d_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 (eg. you may be able to process an 800 residue long sequence and get a result without timing out, which is why no length validation has been added to this program so that you can use the program as is on a more powerful computer.).

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.

The Windows version has implemented VALPRED, whereas the Perl version has implemented VALPRED and VALPRED2 implemented.

The Perl command line version allows you to specify and display the true TMS in addition to the predicted TMS.

The Perl command line version allows you to run multiple sequences in batch mode.

Incidently, the Windows version has the 'VALPRED 3D' implementation of the 3D verification of a protein structure with its REPIMPS and PROFILES3D environments, as described by Dastmalchi et al. 2001. (The 'VALPRED 3D' implementation may need some final attention before general use.) This Perl program does not have the 'VALPRED 3D' implementation.




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 :

VALPRED and VALPRED2 program have been benchmarked at the
Benchmark of Membrane Helix Predictions from Sequence server.


Source Code : perl_valpred_2d_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

Please note that if your sequence is too long for this server (around over 600 residues long), 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)
GRAPH RESIDUE WIDTH : 
GRAPH HEIGHT : 
TMS PREDICTION ALGORITHM : 
OPTIONS FOR VALPRED ALGORITHM :
MINIMUM AREA DIFFERENCE : 
MOVING AVERAGE : 
MIN AV SASA : 
MIN TMS LENGTH : 
MAX TMS LENGTH : 
MIN AV PROFILES3D RANGE : 
MAX AV PROFILES3D RANGE : 
MIN AV REPIMPS RANGE : 
MAX AV REPIMPS RANGE : 
MIN LENGTH DIVIDED BY AREA : 
MAX LENGTH DIVIDED BY AREA : 
MIN SCORE DIFFERENCE : 
OPTIONS FOR VALPRED 2 ALGORITHM :
IF VALPRED2 USED,
SHOW ALL LINES USED BY VALPRED2 : 
MINIMUM AREA DIFFERENCE : 
MV.AV.1 : 
MV.AV.2 : 
MV.AV.3 : 
MV.AV.4 : 
MIN TMS LENGTH : 
MAX TMS LENGTH : 
MAX LENGTH NON-TMS : 
MIN LENGTH NON-TMS : 
MIN NON-TMS SCORE DIFFERENCE : 
MIN NON-TMS AREA : 
TWILIGHT TMS ZONE AREA PER RESIDUE - LOWER LIMIT : 
TWILIGHT TMS ZONE AREA PER RESIDUE - UPPER LIMIT : 
IGNORE TWILIGHT TMS ZONE : 
NO. RESIDUES SEARCH AREA FOR TMS NEIGHBOURS : 
VALPRED2 MIN HELIX LENGTH : 
MIN SCORE DIFF FOR TMS ENDS (MOV.AVG.1) : 
MIN SCORE DIFF. MOV.AVG.1 : 
MIN SCORE DIFF. MOV.AVG.2 : 
MIN AV AREA MOV.AVG.1 : 
MIN AV AREA MOV.AVG.2 : 
DISPLAY OPTIONS :
Profiles 3D :  Show line:
Line colour:
Line label:
Smooth line:
REPIMPS :  Show line:
Line colour:
Line label:
Smooth line:
Both/Overall :  Show line:
Line colour:
Line label:
Smooth line:
Profiles 3D (mv.av.1) :  Show line:
Line colour:
Line label:
Smooth line:
REPIMPS (mv.av.1) :  Show line:
Line colour:
Line label:
Smooth line:
TMS (mv.av.1) :  Show line:
Line colour:
Line label:
Smooth line:
Profiles 3D (mv.av.2) :  Show line:
Line colour:
Line label:
Smooth line:
REPIMPS (mv.av.2) :  Show line:
Line colour:
Line label:
Smooth line:
TMS (mv.av.2) :  Show line:
Line colour:
Line label:
Smooth line:
Profiles 3D (mv.av.3) :  Show line:
Line colour:
Line label:
Smooth line:
REPIMPS (mv.av.3) :  Show line:
Line colour:
Line label:
Smooth line:
Hydrophilic area (mv.av.3) :  Show line:
Line colour:
Line label:
Smooth line:
Profiles 3D (mv.av.4) :  Show line:
Line colour:
Line label:
Smooth line:
REPIMPS (mv.av.4) :  Show line:
Line colour:
Line label:
Smooth line:
Hydrophilic area (mv.av.4) :  Show line:
Line colour:
Line label:
Smooth line:
Transmembrane Segments :  Show line:
Line colour:
Line label:
Smooth line:


Notes about these parameters :

VALPRED uses the area between the REPIMPS and PROFILES3D lines to predict transmembrane segments (TMS). VALPRED performs well at predicting transmembrane helices whilst avoiding false positives. VALPRED2 performs well at predicting predicting small helices, such as in potassium channels, but tends to predict some false positives.

By default, VALPRED2 will question whether area falling within the TWILIGHT TMS ZONE AREA PER RESIDUE - LOWER LIMIT and TWILIGHT TMS ZONE AREA PER RESIDUE - UPPER LIMIT might be a hydrophobic helix in a soluble protein instead of being a membrane helix. If there are no other membrane helices close by, within NO. RESIDUES SEARCH AREA FOR TMS NEIGHBOURS, that have areas above the twilight zone, then it will not be marked as a membrane helix. To display all such hydrophobic helices in soluble proteins, set IGNORE TWILIGHT TMS ZONE to Yes.