Dear Sanjit, use the BD with lots of grains of salt and verify with a real experiment that the found binding pocket is real, else this is waste of money. If you know of a known ligand to interact with your particular protein, you can use this as a test BUT depending what your input model is e.g. NMR or X-ray structure, resolution, conformations of side chains etc. you might not even find a true ligand binding to your protein. VLS is tricky and can serve as a guide but NEVER take it as the only truth for your experiments.
Jürgen ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742<tel:%2B1-410-614-4742> Lab: +1-410-614-4894<tel:%2B1-410-614-4894> Fax: +1-410-955-2926<tel:%2B1-410-955-2926> http://lupo.jhsph.edu On Oct 15, 2014, at 11:11 AM, Sanjit Roy <[email protected]<mailto:[email protected]>> wrote: Dear All I wish to know If the experimental determination of ligand-protein complex structures is difficult to analyze or if the ligand protein complex structure is not known. Then blind docking (BD) and pocket search (PS) calculations would be good in the prediction of binding mode and the location of the pocket of a ligand on the entire protein surface. Sincerely Sanjit Kumar -- *Dr. Snjit Kumar* *Work gives you meaning and purpose and life is empty without it. *
