I want to identify the physicochemical properties of binding pockets of different proteins, as it has reported in some literature that the binding pocket of each protein has different and unique physicochemical property.
http://www.biotec.tu-dresden.de/~bhuang/pdf/JMR.pdf this paper might help
Try Simulation Plus ADMET predictor
http://www.simulations-plus.com/Products.aspx?pID=13
Open Eye is been used to study ligand binding for drug design.
http://www.eyesopen.com/products
With the openeye tools, you will initially require an academic license (for academic users). The next challenge will be learning to use the tools (each tool comes along with a manual), the learn how to manage file types, etc and how to interpret the results.
With MOE, you can use the sitefinder module to locate a number of potential binding sites and their properties. Then use visual inspection to locate the possible binding site of the ligand in question.
Thank you Mr Christopher and Mr Fidele for your guidance and valuable time.
Mr Fidele I have tried the option of MOE as you have mentioned in your mail, but i think there is some problem with the site (the link I am trying is http://www.chemcomp.com/), will you please provide me the appropriate link for the same.
Thanks in advance.
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