Hi, Yes, SPASM works very nicely for doing a comparison like this. See Fig 3 in this publication of ours where we performed a similar analysis: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116655/ Best, Debanu -- Debanu Das
On Wed, Jan 8, 2020 at 3:28 PM Rigden, Dan <[email protected]> wrote: > Dear Lei > > > You can use ASSAM for this > > > http://27.126.156.175/assam/ > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394286/ > > In the past I've also used SPASM locally for this > > http://xray.bmc.uu.se/usf/spasm.html > > but I think you'll need to generate your own up to date database to search. > > > Best wishes > > Dan > > > ------------------------------ > *From:* CCP4 bulletin board <[email protected]> on behalf of Zheng, > Lei <[email protected]> > *Sent:* 08 January 2020 15:57:23 > *To:* [email protected] > *Subject:* [ccp4bb] Searching similar local structural conformations > > > Dear CCP4ers, > > > > We identify a potential ion binding site formed by four residues in a > structure. I want to search if any other structures have a similar local > residual geometry. Is there any programs to perform such a searching? For > example, to search in Protein Data Bank using coordinates of the binding > site residues? I appreciate your suggestions. > > > > Happy New Year! > > Lei > > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
