[ccp4bb] how to interpret DALI search results
Dear ALL; After we solved our structure by anomalous scattering, we did a DALI search. Here are the results but it is not easy to draw meaningful conclusions whether our structure represents a novel fold or is homologous to others. Basically the Z-score is between 2 and 6.4 since our structure only contains 130 residues. Sequence identity is between 5 to 15%. The RMSD of structural alignment is between 2.5 to 6 angstrom. Any suggests to interpret the DALI results? Many thanks, Jerry McCully
Re: [ccp4bb] how to interpret DALI search results
if this is the first (or second, or third) time you do a DALI search, take the list output from DALI, start from the top and superpose each structure with yours and look at the superpositions with your favourite superposition software. This is very educational and the only way you get a feeling for what numbers mean. Quoting Jerry McCully: Dear ALL; After we solved our structure by anomalous scattering, we did a DALI search. Here are the results but it is not easy to draw meaningful conclusions whether our structure represents a novel fold or is homologous to others. Basically the Z-score is between 2 and 6.4 since our structure only contains 130 residues. Sequence identity is between 5 to 15%. The RMSD of structural alignment is between 2.5 to 6 angstrom. Any suggests to interpret the DALI results? Many thanks, Jerry McCully Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: mjvanra...@cnb.csic.es
Re: [ccp4bb] how to interpret DALI search results
...I meant visualisation software of course... Quoting VAN RAAIJ , MARK JOHAN: if this is the first (or second, or third) time you do a DALI search, take the list output from DALI, start from the top and superpose each structure with yours and look at the superpositions with your favourite superposition software. This is very educational and the only way you get a feeling for what numbers mean. Quoting Jerry McCully: Dear ALL; After we solved our structure by anomalous scattering, we did a DALI search. Here are the results but it is not easy to draw meaningful conclusions whether our structure represents a novel fold or is homologous to others. Basically the Z-score is between 2 and 6.4 since our structure only contains 130 residues. Sequence identity is between 5 to 15%. The RMSD of structural alignment is between 2.5 to 6 angstrom. Any suggests to interpret the DALI results? Many thanks, Jerry McCully Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: mjvanra...@cnb.csic.es Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: mjvanra...@cnb.csic.es
Re: [ccp4bb] how to interpret DALI search results
On Tuesday, June 12, 2012 02:29:13 pm Jerry McCully wrote: Dear ALL; After we solved our structure by anomalous scattering, we did a DALI search. Here are the results but it is not easy to draw meaningful conclusions whether our structure represents a novel fold or is homologous to others. I don't think the question is it homologous can ever be answered by a DALI score, whether it is high or low. For that you need to think about sequence families, inferred evolutionary history, shared function, etc. If your structure has a biological function related to that of your DALI hit, I'd be inclined to consider seriously whether they could be distant homologs. If not, I doubt you will convince anyone based only on a vaguely similar fold. A sequence identity of 15% is really low, but that is presumeably only a pairwise comparison. You should try PSIBLAST or similar to see if both your protein and the DALI hit are recognizably members of the same sequence family or superfamily. Ethan Basically the Z-score is between 2 and 6.4 since our structure only contains 130 residues. Sequence identity is between 5 to 15%. The RMSD of structural alignment is between 2.5 to 6 angstrom. Any suggests to interpret the DALI results? Many thanks, Jerry McCully -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
