CCL: prediction of peptide structures and protein-protein docking

 Sent to CCL by: "Cristian Bologa" []
 Hi Guiyu,
 Given the complexity of your problem, you should probably try to incorporate in
 the modeling experiment all the experimental knowledge you can get (from
 literature, your colleagues, etc). For example, before trying to model de novo
 the structure of your peptide, you can try your luck by doing a sequence
 similarity search on the protein data bank (PDB) to see if there are any
 peptides or (parts of) proteins similar to your peptide.
 For the docking part, you might want to find out if other similar peptides have
 been tested on that receptor, if there are any key residues important for
 binding to the receptor, if the peptide has been tested on any receptor mutants,
 etc. You could also use that information in the next iteration of peptide
 structure refinement.
 Also if the sequence of the peptide is confidential you probably do not want to
 upload it to any public server.
 Cristian Bologa, Ph.D.
 Research Associate Professor,
 Div. of Translational Informatics,
 Dept. of Internal Medicine,
 Univ. of New Mexico, School of Medicine,
 Innovation Discovery & Training Center, MSC10 5550,
 700 Camino de Salud NE, Albuquerque, NM 87131
 tel: +1-505-925-7534
 >>> "Guiyu Zhao guiyu.zhao(0)"
 <> 8/26/2012 2:30 AM >>>
 Sent to CCL by: "Guiyu  Zhao" [guiyu.zhao{:}]
 Dear CCL colleagues,
 I'm trying to fulfill a request from my colleagues about a 17-membered peptide.
 They want to get a rough idea about the peptide's 3D structure and, if possible,
 the binding pose with a cell receptor.
 I feel the task is chellenging for me not only because I'm a modeler on small
 molecules and not familiar with protein modeling, but also because we are lack
 of commercial tools to do peptide structure prediction and protein-protein
 docking. So first of all, is there any free tool to do such calculations?
 RosettaDcok and BioLuminate from Schrodinger Inc. are not available to me. Then,
 is it reallistic to model a peptide's 3D structure without knowing anything
 about its secondary structure (my colleagues only provided me its sequence)?
 Thank you in advance for any response.
 Kind regards,
 Guiyu Zhao