A blog about free research software, alternative to commercial paid software.

One way to help people is to share your knowledge with those who could benefit from it. As a researcher , constant effort to solve scientific problems have exposed me to various scientific resources that can be accessed free of charge. Especially these knowledge is useful to labs and institution unable to access expensive software or novice users due to lack of expertise. In this blog, I have provided a comprehensive list of freely available softwares, alternative to commercial software. I shall share with you all that I have learned, as I make the changes or learn something new, I shall document them. Hope this blog will help those finding the way………….

Research software and books

Dec 20, 2010

Drug designing

Argus Lab

A molecular modeling, graphics, and drug design program. ArgusLab is freely licensed.

Website to download: http://www.arguslab.com/index.htm


AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates ordrug candidates, bind to a receptor of known 3D structure.

Website to Download: http://autodock.scripps.edu/


Website to Download: http://dock.compbio.ucsf.edu/


Hex is an interactive molecular graphics program for calculating and displaying feasible docking modes of pairs of protein and DNA molecules. Hex can also calculate protein-ligand docking, assuming the ligand is rigid, and it can superpose pairs of molecules using only knowledge of their 3D shapes.

Website to download: http://hex.loria.fr/manual/hex_manual.html


ZDOCK is arigid-body docking program, and RDOCK is a refinement program, . ZDOCK uses a fast Fourier transform to search all possible binding modes for the proteins, evaluating based on shape complementarity, desolvation energy, and electrostatics. The top 2000 predictions from ZDOCK are then given to RDOCK where they are minimized by CHARMM to improve the energies and eliminate clashes, and then the electrostatic and desolvation energies are recomputed by RDOCK (in a more detailed fashion than the calculations performed by ZDOCK).

Website to Download: http://zdock.bu.edu/software.php


Openeye is an excellent molecular modelling package and has following capabilities. 1) Prepare the input compounds by removal of undesirables and application of a variety of charge models.
2) Generates high quality 3D conformer ensembles. Searches compound libraries for 3D shape (and chemistry) similar molecules. 3) used to refine the by electrostatic similarity. 4) Searches fragment databases for bioisosteric replacements using 5) Powerful graphical interface for visualization and effective communication of results, which can then export live into PowerPoint® presentations or web pages. 6 ) A standalone application for ligand fitting to crystallographic density.

Website to Download: http://www.eyesopen.com/academic-request