Re: [ccp4bb] domain boundary, new fold, structure-based sequence alignment
On Sun, Oct 18, 2009 at 10:00 AM, Shaun Lott wrote: > In my experience, DALI can be better than SSM at detecting distant > structural similarities. this is interesting. Do you take into account that, in difference of DALI, SSM has a control on the remoteness of structural hits that it delivers? By default, it looks only at fairly similar hits. It grabs more hits as you pull the similarity threshold down. And if you set that similarity threshold zero, nearly every query gathers half of PDB as potential targets - because small features are shared between many structures. I would be very curious to see an example where SSM *is not able* to catch something that DALI catches - leaving aside SSM limitations like presence of secondary structure and having at least 2-3 SSEs in the common motif. Eugene > You might also want to try CE. To decide if a fold > is 'new' rather than 'old but decorated' often boils down to a somewhat > subjective call, but asking Alexei Murzin is as good a way as any to decide > :-) > > For domain definition, try http://pdomains.sdsc.edu/ which offers a handy > interface for comparing a number of different methods for automatic domain > calling. > > hope this helps > > Shaun >
Re: [ccp4bb] domain boundary, new fold, structure-based sequence alignment
In my experience, DALI can be better than SSM at detecting distant structural similarities. You might also want to try CE. To decide if a fold is 'new' rather than 'old but decorated' often boils down to a somewhat subjective call, but asking Alexei Murzin is as good a way as any to decide :-) For domain definition, try http://pdomains.sdsc.edu/ which offers a handy interface for comparing a number of different methods for automatic domain calling. hope this helps Shaun
Re: [ccp4bb] domain boundary, new fold, structure-based sequence alignment
On Friday 16 October 2009 15:49:16 Demet Arac-Ozkan wrote: > 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. TLSMD analysis is a possibility. It will not give a definitive answer to the question "one domain or two?", but it may tell you where the boundary should be drawn if you do decide to treat it as two. http://skuld.bmsc.washington.edu/~tlsmd/ > 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 > -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] domain boundary, new fold, structure-based sequence alignment
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 : CCP4BB@JISCMAIL.AC.UK > 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 > >
[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
