Hi Francesco, There is a Dock Prep tool in Chimera: it cleans up the receptor (or ligand) structure, adds hydrogens, associates atoms with partial charges (Amber for standard residues, Antechamber calculations for nonstandard), and writes it out in Mol2 format. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ dockprep.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/ addcharge.html However, it does not do anything to help find binding sites or to divide up a very large structure. It is not involved in the surface and sphere calculation steps. In the future we would like to better integrate Chimera with those steps, but it hasn't been done yet. Using the dock-related programs, I imagine you would calculate sets of spheres that fill each large pocket of the protein, then calculate a scoring grid for each pocket and dock separately to the different pockets (as suggested by Dr Brozell). The process would be similar to what is shown in the dock tutorials, just done multiple times for the different pockets. There are several separate tools or web servers that you can use to try to identify pockets if they are not already obvious. For example, the Surfnet tool in Chimera: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfnet/ surfnet.html or the CASTp web server: http://sts.bioengr.uic.edu/castp/ I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Oct 2, 2007, at 3:12 AM, Francesco Pietra wrote:
Hi Elaine: That you mention was wonderful discovery.
Coming closer to my work: What I want to do at the moment is examining if Dock can identify how certain natural products (lipophilic molecules of about 180 first-row atoms) interact with a large protein. I know experimentally that there is interaction, nearly surely with the protein itself and not merely a destruction of the bilayer. Though, I have no idea about the protein region responsible.
I have already carried out a conformational search for my natural products by simulated annealing with an algorithm that calls Amber9. Parameter and coordinate files for Amber9 were built with Antechamber. X-ray diffraction data at medium resolution for the protein are available.
The tutorials on DOCK does not consider take such a problem (the tutorial starts from a protein-ligand complex elucidated by X-ray diffraction). Professor Brozell suggested that the size of the protein may put a practical limit on the size of Dock's grid, though, one approach would be to divide and conquer the big protein binding sites into subsets that would be processed separately.
My question is: can Chimera help such preparation of the protein for docking?
Thanks francesco