Sunday, May 31, 2009

A GUI to MODELLER

Homology modeling has become a key component in structural bioinformatics for prediction of the three-dimensional structure of proteins from their sequences due to availability of huge amount of protein sequence data and the growing number of known structures. It becomes even more useful when constraints from X-ray diffraction or NMR are not yet available. Many tools have been developed for homology modeling out of which the most popular and widely used is MODELLER developed by Prof. A. Sali and co-workers. MODELLER stands apart from other packages due to its free availability, powerful features and reliable results. But most users find it a bit difficult to start with MODELLER as it is command line based and requires knowledge of basic Python scripting to use it efficiently. A freely available GUI for this great package would thus be very helpful to exploit the powers of this homology modeling package by everyone. EasyModeller is a frontend graphical interface to MODELLER developed using Perl/Tk, which can be used as a standalone tool in windows platform with MODELLER and Python preinstalled. The aim of this tool is to help inexperienced users as well as regular users to perform modeling, assessment, visualization, and optimization of protein models in a simple and straightforward way. EasyModeller can produce 3D structural models of proteins from sequence and given template(s) information using MODELLER in backend. A detailed help is provided for every step with robust error handling.

I have developed a GUI to MODELLER ,which is a standalone executable that runs on windows platform and needs you to have just MODELLER and Python installed in your system.You need not require to know any scripting,just a user friendly GUI guides you through the entire process of modelling.Four modelling options are available :Model using single template,model using hetroatom,model using multiple templates and loop modelling. This is the first version called EasyModeller 1.0 and might have some bugs. A modified version would be available very soon.

People interested can mail me at kuntal.bhusan@gmail.com
Link to download :
click here
Kuntal Kumar Bhusan
M.Tech Bioinformatics
University of Hyderabad
India

10 comments:

Anonymous said...

What are the inputs required for your tool?

kuntal said...

You just need to paste the query sequence in the input window and load the template PDB/PDBs.The tool(called EasyModeller) will automatically model the structure from the sequence by running Modeller in the backend.

Anonymous said...

It is a really impressive work and a very important addition in this field. This will help a lot of people and will provide faster modelling environment to them.

robert said...

good work

cool_rock said...

Thnx 4 d GUI
even i m working to develop its GUI....
It l help me a lot....

akash said...

very nice software.waiting for the new version.

manish said...

Hey i just installed the new version...its really cooll....too good work

Nia LaNiaz said...

Hi kuntal.. do you know how to run modeller9.9 in linux?..i've prob about usage mod9.9 script?..i hope u can help me.

kuntal said...

@Nia LaNiaz

You can install modeller using yum or apt get and python as well.To run a python script you need to use :
>python

BioInfo said...

I have downloaded EasyModeller but unable to view Alignment file. It's empty.

OS: Windows 7
Modeller: 9v7 (C:\Program Files)
Python: 2.7 (C:\)

Pasted the sequence, Selected the template, SALIGN, Perform Alignment, View Alignment (The alignment file is empty)

Keep up the good work!

Thanks!