From owner-chemistry@ccl.net Sun Feb 22 03:49:00 2009 From: "Gerard Pujadas gerard.pujadas-$-gmail.com" To: CCL Subject: CCL: Is there any database that collects which ligands coordinates (derived from the PDB files) are reliable? Message-Id: <-38700-090222034823-31023-MpwXBd0KjV+GnmR/KE8sCw===server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=0015174c142208179704637df20d Date: Sun, 22 Feb 2009 09:48:09 +0100 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas:-:gmail.com] --0015174c142208179704637df20d Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCL list subscribers, for those who are interested in the answers I have had to my last friday question, please find here the answer I had from Gerard J. Kleywegt when I sent the same question to the PDB list: First, you probably want to read this paper: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18598022 Second, real-space fit statistics (that tell you how well ligands fit to their density) are available on a per-entry basis from EDS ( http://eds.bmc.uu.se/eds/) and on a per-ligand basis from HIC-Up ( http://xray.bmc.uu.se/hicup/) or ValLigUrl ( http://eds.bmc.uu.se/eds/valligurl.php). Say, you're interested in FK5 (ascomycin). You can enter this in ValLigUrl and will get a list with all instances in the PDB. Click on the column header "RSR" and they will be sorted by Real-Space R-value. Ignore all the ones without such a value. In this case, the first 6 instances have RSR values and they are all between 0.07 and 0.15 in structures with resolution between 1.6 and 2.5A. Click on the PDB code to go to the EDS entry or the residue number to view model and density in the AstexViewer. You can then decide which ones are sufficiently well-modeled for your purposes. For an EMBO Course at the EBI last year I prepared a little practical that may be of use too: http://xray.bmc.uu.se/embo/ligandtut/ --Gerard ****************************** ************************************ Gerard J. Kleywegt Dept. of Cell & Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:gerard,,xray.bmc.uu.se ****************************************************************** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ****************************************************************** Have a nice weekend !!! Gerard --0015174c142208179704637df20d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL list subscribers,

for those who are interested in the answe= rs I have had to my last friday question, please find here the answer I had= from Gerard J.  Kleywegt when I sent the same question to the PDB lis= t:


First, you probably want to read = this paper: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=3DRetrieve&= amp;db=3Dpubmed&dopt=3DAbstract&list_uids=3D18598022

Second, real-space fit statistics (that tell you how well ligands fit to their density) are available on a per-entry basis from EDS (http://eds.bmc.uu.se/eds/) = and on a per-ligand basis from HIC-Up (http://xray.bmc.uu.se/hicup/) or ValLigUrl (http://eds= .bmc.uu.se/eds/valligurl.php).

Say, you're interested in FK5 (ascomycin). You can enter this in ValLigUrl and will get a list with all instances in the PDB. Click on the column header "RSR" and they will be sorted by Real-Space R-v= alue. Ignore all the ones without such a value. In this case, the first 6 instances have RSR values and they are all between 0.07 and 0.15 in structures with resolution between 1.6 and 2.5A. Click on the PDB code to go to the EDS entry or the residue number to view model and density in the AstexViewer. You can then decide which ones are sufficiently well-modeled for your purposes.

For an EMBO Course at the EBI last year I prepared a little practical that = may be of use too: http://xray.bmc.uu.se/embo/ligandtut/

--Gerard

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*****= *******************************
                    &nbs= p;     Gerard J.  Kleywegt
  Dept. of Cell & Molecular Biology  University of Uppsala                   Biomedical = Centre  Box 596
                  SE-751 24 U= ppsala  SWEDEN

   h= ttp://xray.bmc.uu.se/gerard/  mailto:gerard,,xray.bmc.uu.se
******************************************************************
  The opinions in this message are fictional.  Any similarity   to actual opinions, living or dead, is purely coincidental.
******************************************************************

Have a nice weekend !!!

Gerard
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