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
