Monday, July 23, 2012

EasyModeller 4.0 : A new GUI to MODELLER

EasyModeller 4.0 introduces a fresh new GUI for Homology Modelling using MODELLER in the backend and available for both Windows and Linux platform. This version has several new features integrating all the goodies of EasyModeller 3.0 which was only available for LINUX.

The highlighted features of this version are :

1. Tab based logical Modelling steps with extensive error handling
2. Allows to load unlimited number of templates
3. A colorful alignment viewer and also with an inbuilt alignment editor
4. On the fly MODELLER code editing ( generated MODELLER scripts can be edited as per user's need and run from within the tool). This feature would be most useful for advanced MODELLER users.
5. Inbuilt DOPE profile Viewer, Ramachandran Plot viewer, Loop Modelling, Basic model optimization and dynamics for a selected Model.

DOWNLOAD Link :  Click here

PLATFORMS SUPPORTED : 32 bit LINUX and WINDOWS
(I have also tested it to work on a 64 bit Windows 7 Home Basic with Modeller 9v11 and Python 2.7.3)

If you face any problems please use this Google Groups forum to ask questions : Click here

For a detailed tutorial and manual : click here
To discuss on the topic : click here


Tab 1 : Loading Sequence and Template





Tab 2 : Aligning the Templates




Tab 3 : Aligning the Query with Templates



Tab 4 : Generating the model



Additional Functions

1. On the fly MODELLER Code Editing


2. Interactive Ramachandran Plot Viewer



3. Backend code output


4. Automatically displays the model using default PDB viewer




For a detailed tutorial and manual : click here

Monday, August 24, 2009

EasyModeller 2.0 released

Click on the image to enlarge it


I am here again with a new release of the Modeller GUI called EasyModeller 2.0. Now you can use this tool for quality scientific research in Homology Modelling and cite it as it is published in the reputed international journal Biomed Central (BMC) (publication link).Added features over the previous version includes :
  •  Better error handling at every step of modelling.
  •  Working directory for each session.
  •  Automatic alignment generation.
  •  Supports upto 6 templates at a time.
  •  Added manual and automatic loop modelling of the models.
  • Support for visual alignment editing ( using BioEdit for EasyModeller 2.1 ).
  •  Model optimization.
  • Basic molecular dynamics simulation using customized parameters.
Besides this, the tool is very helpful especially for beginners in homology modelling as the starting objective for developing it was to graphically teach the process of homology modelling using MODELLER to inexperienced users who are unaware of python scripting.


new For LINUX users EasyModeller 3.0 is available with a much wider range of feature. Click here to know more.


For troubleshooting and bug report :
mailto : kuntal.bhusan@gmail.com
or post a comment here




Manual


 Click here to view manual.


Requirements


  • The hardware requirements are same as that required for running MODELLER.
  • You should have MODELLER and PYTHON preinstalled in your system to run the application. 
  • MODELLER should be installed in the default location (i.e: C://Program Files/Modeller/..)
  • To display the energy profile plots Microsoft Excel should be installed.
  • If you are running WINDOWS VISTA or WINDOWS 7 and have kept EasyModeller application in the Operating System partition (C://) then to run the application Right click on the icon on desktop and select "Run as administrator", otherwise the OS might not give permissin to create new working diretory and you won't get any output.
  • Any version of MODELLER before and including 9v7 is supported N.B : Some features of Modeller 9v8 is not supported so it is advised to use 9v7. A 9v8 compatible   version of EasyModeller will be launched soon.
  • Python 3.11 is NOT SUPPORTED use either 2.6 or 2.5 because they offer better support to third party softwares.
  • Some 64 bit windows OS seem to be incompatable but works in many cases if the proper 64 bit MODELLER is installed.
  • I have successfully tested EasyModeller to run with Modeller9v9 and Python 2.7 in a 32 bit Windows 7 system and  Rasmol as the default PDB viewer.
Any system which is able to run the manual version of MODELLER is fully qualified to run EasyModeller.

To DOWNLOAD

Visit : http://bioinformatikz.googlepages.com/

Publication Link


If you are using EasyModeller for your research work, please cite :


Publication Link : click here
Pubmed ID : 20712861
EasyModeller: A graphical interface to MODELLER.
Kuntal BK, Aparoy P, Reddanna P.
BMC Res Notes. 2010 Aug 16;3(1):226.



Related citations with EasyModeller 



Cardona F, Sánchez-Mut JV, Dopazo H, Pérez-Tur J.
Hum Mutat. 2011 Apr;32(4):369-78. doi: 10.1002/humu.21444.
PMID:21412950

Hansen KB, Traynelis SF.
J Neurosci. 2011 Mar 9;31(10):3650-61.
PMID:21389220


Phosphorylation Alters the Interaction of the Arabidopsis Phosphotransfer Protein AHP1 with Its Sensor Kinase ETR1.
Scharein B, Groth G
PLoS ONE , 2011,6(9): e24173. 
doi:10.1371/journal.pone.0024173


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