By the way, I'll extend that question: the validation software Verify3D assigns not only buried state but also polar fraction and secondary structure, using the probability of finding given residues in the different "environment" defined when combining all this information to calculate a "score" of protein regions, which could identify, for example, sequence misthreading. The program is rather old (1991) and, aside from the automated validation site at UCLA (which just let you upload a PDB and get the scores), I haven't found a web page for it. Is there available code to assign residues to one of those "environments" and updated probabilities of finding amino acids in each one?
Lucas Wei Huang wrote: > Hi all, > > Do someone know a tool which could identify the > location of the sequence in > tertiary structure known protein, that is the > sequence is on the surface or > in the > core? Usually we use visualization tools, such as > RasMol, VMD, to identify this > by our eyes. But I don't know whether there are > tools that we could input PDB > file and the sequence only, then the computer > tells us the sequence is on the > surface or in the core. __________________________________________________ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/
