Hi When you said that psiBLAST did not return results, did you run it against pdb or against nr? I recently found a case where a blast against pdb return nothing, but a psiblast against nr return results and some of them had structures. We were able to made a very good model (we end up having the xtal structure so we could check) using hmmer's jackhmmer against uniprot and using the best result with known structure in the final alignment (-A option) and the % of identity was below 30.
I hope this helps.
OCS
Oscar Conchillo Solé Group of Computational Biology and Proteomics IBB Data Center Manager and Linux Sysadmin Institut de Biotecnologia I Biomedicina (UAB) mail: txino@bioinf.uab.es telf: 0034 93581 4431; 0034 93586 8939
On 07/21/2014 07:23 PM, Modeller Caretaker wrote: > On 7/20/14, 4:51 AM, Vishal Nemaysh wrote: >> I have faced a problem during 3D structure prediction of my target >> protein of interest. The length of the protein sequence is (1106 amino >> acids). Sir i have tried to find out some templates for covering the >> whole query sequence during BLAST or psiBLAST. But there is no any >> single template or multiple templates are found to occupied this whole >> query sequence. > > In that case your only options are to try more sensitive template > selection methods (e.g. profile based) or to build models of only part > of the sequence. > > Ben Webb, Modeller Caretaker