Re: [ccp4bb] quaternary structure comparison
Dear Eike, depending on what your structure is - you can try interface search in PISA (google on "ebi pisa"). Select the most "representative" interface in your complex (the one that makes the non-standard arrangement) and see whether there are similar interfaces in the PDB. It shouldn't be a too long list, you may then shorthen it to structures with given oligomeric state and finally check them by eye. Cheers, Eugene. On Mon, 15 Jun 2009, Eike - Christian Schulz wrote: Dear All, I solved a structure that has a very common tertiary structure motif but it appears as if the arrangement of the monomers is somewhat non-standart¹. Of course I performed a DALI search, which resulted in a great number of hits due to the similarity of the tertiary structure (Z¹s: 250 >8; 100 > 10). In order to check whether this arrangement that I see is something new I would like to perform a quaternary structure comparison. Is there any such tool available? A Google search wasn't very conclusive. Or is there a clever combination of available resources? Kind regards Eike
Re: [ccp4bb] quaternary structure comparison
The human intelligance system "Alexey Murzin" of the LMB in Cambridge comes to mind - helpful and knowledgable about "all" known folds. Mark Quoting Roberto Steiner : Hi Eike, PISA (http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html) or SCOPPI (http://www.scoppi.org ) might be useful. Interested in hearing about other alternatives. Best wishes Roberto On 15 Jun 2009, at 21:28, Eike - Christian Schulz wrote: Dear All, I solved a structure that has a very common tertiary structure motif but it appears as if the arrangement of the monomers is somewhat ‘non-standart’. Of course I performed a DALI search, which resulted in a great number of hits due to the similarity of the tertiary structure (Z’s: 250 >8; 100 > 10). In order to check whether this arrangement that I see is something new I would like to perform a quaternary structure comparison. Is there any such tool available? A Google search wasn't very conclusive. Or is there a clever combination of available resources? Kind regards Eike --- Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail roberto.stei...@kcl.ac.uk
Re: [ccp4bb] quaternary structure comparison
Hi Eike, PISA (http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html) or SCOPPI (http://www.scoppi.org ) might be useful. Interested in hearing about other alternatives. Best wishes Roberto On 15 Jun 2009, at 21:28, Eike - Christian Schulz wrote: Dear All, I solved a structure that has a very common tertiary structure motif but it appears as if the arrangement of the monomers is somewhat ‘non-standart’. Of course I performed a DALI search, which resulted in a great number of hits due to the similarity of the tertiary structure (Z’s: 250 >8; 100 > 10). In order to check whether this arrangement that I see is something new I would like to perform a quaternary structure comparison. Is there any such tool available? A Google search wasn't very conclusive. Or is there a clever combination of available resources? Kind regards Eike --- Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail roberto.stei...@kcl.ac.uk
[ccp4bb] quaternary structure comparison
Dear All, I solved a structure that has a very common tertiary structure motif but it appears as if the arrangement of the monomers is somewhat non-standart¹. Of course I performed a DALI search, which resulted in a great number of hits due to the similarity of the tertiary structure (Z¹s: 250 >8; 100 > 10). In order to check whether this arrangement that I see is something new I would like to perform a quaternary structure comparison. Is there any such tool available? A Google search wasn't very conclusive. Or is there a clever combination of available resources? Kind regards Eike
