Hi, Apparently your QCOPS link below is for a structure navigator that requires flash. I guess I'm looking for something like the result here,
http://nar.oxfordjournals.org/cgi/reprint/gkm264?ijkey=hqzSJIdl8y6jwUO&keytype=ref ( without even wanting the BLAST results ) but I want a text output to feed to other programs. Can I somehow post a pdb file to your server and get back a (text) list of molecules with similarly shaped and colored ( by atoms that make up the cavity walls ) cavities? This relates to my previous series of posts on the need for an API as opposed to just a human web interface. I may want to use scripts or automated processes to sort through many candidates before using an interactive navigator. I was trying to figure out what databases exist that contain simplified shape and environment information on cavities or surfaces for finding "accidental" ( without any obvious sequence homology) matches or near matches of function. You did mention things like conformations or modifications that distort the shape. Obviously, you would like to find things that are close but not exact and try to figure out what implications these may have for function. Thanks. > Date: Wed, 2 Apr 2008 10:52:07 +0200 > From: [EMAIL PROTECTED] > > Indeed, the structural similarity of dehydrosqualene synthase (PDB codes: > 2zco, 2zcp, 2zcq, 2zcr, 2czs) and humane squalene synthase (PDB codes 1ezf) > is striking in the view of their low sequence identity. TopMatch-web yields > an RMS of 3.5A and a sequence identity of 11% if the respective chains A are > compared. > > Talking about finding such similarities: one tool that is really helpful for > this task is the qCOPS web service (some advertising again ;-) at > http://navi.services.came.sbg.ac.at/bin/qCOPS.html > For further information on qCOPS, see > Sippl et al. > A Discrete View on Fold Space > Bioinformatics, 24, pp. 870-871 (2008) > (Open Access: > http://bioinformatics.oxfordjournals.org/cgi/reprint/btn020?ijkey=7zgnEsdKQIEfrN7&keytype=ref) > > Best regards, > -Markus > > On Die, 01 Apr 2008, Mike Marchywka wrote: >> >> http://www.nature.com/nrd/journal/v7/n4/full/nrd2554.html >> > _________________________________________________________________ Use video conversation to talk face-to-face with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_video_042008 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
