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


6 comments:

Anonymous said...

It is useful to try everything in practise anyway and I like that here it's always possible to find something new. :)

Antônio Marinho said...

Great Work!

Antônio from Brazil

ice-man said...

nice work Kuntal...but why use modeller instead of i-tasser which i thought ranked No.1 in the Casp rankings in 2010

Tomas said...

It would be useful to have a version for Mac too. Great GUI. Thank you.

kuntal said...

Sure Tomas...I will try to do it....but since I don't have a Mac system, its a bit difficult but I will try to do the same

dhmallon said...

Does anyone know if Easymodeller works with a 64 bit version of linux?

...I am having quite some trouble finding a GUI for Modeller on linux, should Esaymodeller not work on 64 bit linux..

Many thanks