Dear coallegues, I have a protein X without experimentally-solved 3D structure, but with a lot of data on its' secondary structure organization (in other words, I know the conformation (secondary structure) of each residue). I wonder how can I force the protein regions to fold into specific type of secnodary structure upon modeling. On the basis of sequence similarity I have found a suitable templates only for a part of the target proteins, but I'd like to create a full-size model. I don't need a very high quality model at the moment, just a stucture with a correct overall fold.
I know that MODELLER allows to set s.s.restraints, but they do not guarantee the creation of the necessary secondary structure in all regions.
1) Are there any software tools that perform de novo modeling of protein 3D strucutre and allow to set specific sec.str. for each residue?
2) Are there software tools that can find templates on the basis of secondary structure organization?
Thanks in advance for any helpful suggestions!
Hello!
If you would use loopmodel optimization in MODELLER, it will force many regions to coiled structure, so it could be useful if some of the secondary structures are definitely loops (coils).
I think in another case you can either use ab initio prediction servers like QUARK, TASSER, LOMETS, MUSTER, etc. to model a part of your protein which doesn't have homologs in PDB, or: generate a set of peptides in canonical conformations on PepBasic3D (http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py?form=HCA#forms::PepBasic3D) or in any 3D viewer which has this function and use the results of modeling as additional templates to model your protein. Could I have a look onto alignments and secondary structure of target and template?
Best regards, Azat.
i think u can follow I-tasser for this purpose and you can get a 3D structure of entire protein sequence as well relevant to the secondary structure.
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