Hello Abeer, If there is some ligand bound or modeled into the site, you can certainly use Chimera to identify the residues that contact the ligand and/or form H-bonds with it. This is done, for example, in the Structure Analysis and Comparison tutorial using the "Find Clashes/Contacts" and "FindHBond" tools: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ findclash.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ findhbond.html> If you only have the protein and no knowledge of where the active site is, however, Chimera does not predict the location of the active site. There are many, many Web servers that try to predict active sites or important residues given a structure, but I do not have a list of these, sorry. A couple of relevant Web servers that have a connection to Chimera are: (1) CASTp - finds pockets, often the largest is the active site (if you get results e-mailed to you, you can view them in Chimera) <http://sts.bioengr.uic.edu/castp/calculation.php> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html> (2) ConSurf - finds related sequences, makes sequence alignment, shows residue conservation by coloring the structure; often the highly conserved residues are functionally important (one option is to show results in Chimera) <http://consurf.tau.ac.il/> <http://www.cgl.ucsf.edu/chimera/consurf/consurf.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 3, 2009, at 3:56 AM, Abeer Shokeer wrote:
Hello I have a model structure of my protein and I would like to determine which residues that could take part in active site. Can I do that with Chimera? Thanks for your help Abeer