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SSM is your friend there: http://www.ebi.ac.uk/msd-srv/ssm HTH, Fred. > Message du 17/10/09 00:59 > De : "Demet Arac-Ozkan" > A : [log in to unmask] > Copie à : > Objet : [ccp4bb] domain boundary, new fold, structure-based sequence alignment > > > Dear All, > > I have a few questions about protein structure and fold. I will appreciate your suggestions: > We have the crystal structure of a protein and it looks like it might be a new domain. > > 1) Our structure looks like there are two domains however there are some close interactions between the two so we are not sure if we should define it as a single domain or two domains. I am looking for a program where I can enter a pdb file and get out domain boundaries based on the structure. For example something that can do a dot plot of the distances between residues? > > 2) We are wondering whether distant homologues of this protein also have this domain however sequence alignments are not reliable because there is little sequence identity. For doing structure-based sequence alignments, which programs can be used (other than SALIGN)? > > 3) What is the best way to decide whether a structure contains a new fold or not? For example if DALI z scores are about 8 (half of the domain is similar to one protein, the other half is similar to another protein), would you call it a new fold? > > Thanks a lot in advance, > > Demet Arac > >