Looking For A Molecular Visualization Software To Study Binding Sites Of A Protein

Question

[anonymous]

Hi all, I am new to bioinformatics. I am interested in studying binding sites of proteins at the molecular level. I want to know is there any software by which I can get the molecular insight of the binding sites like what types of bonds are present (e.g. H-bond, pi bond, electrostatic) What atoms are involved? What part of the amino acid is involved: amine (-NH2), carboxylic acid (-COOH) groups or the side chain?

Answer 1

[Diwan]

VMD and Chimera are some freely available softwares. Check links below:

VMD

Chimera ucsf

Pymol is the best visualizer. But I am not sure whether it is free anymore.

-Diw

[quentin.delettre]

Pymol : http://sourceforge.net/projects/pymol/