From owner-chemistry@ccl.net Tue Jul 17 18:55:00 2012 From: "David A Mannock dmannock###ualberta.ca" To: CCL Subject: CCL: Any alternative to the TOPS server for drawing topological diagrams for PDB files? Message-Id: <-47217-120717150616-4571-eqbexNY9/giggKLUfHlBDg(-)server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=f46d04071785d183e104c50b3cac Date: Tue, 17 Jul 2012 13:06:02 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock{}ualberta.ca] --f46d04071785d183e104c50b3cac Content-Type: text/plain; charset=ISO-8859-1 A quick Google search using "Tops protein server" found the following sites. The first is a new link to the new TOPS server at Glasgow. Hope this helps you. Not all links on the home page are active. David http://www.brc.dcs.gla.ac.uk/projects/tops/ http://balabio.dcs.gla.ac.uk/drg/compare.html http://www.bioinf.org.uk/topscan/ http://fatcat.burnham.org/TOPS/ http://bioinformatics.burnham.org/pages/servers/ http://www.biochem.ucl.ac.uk/~roman/links/index.html On Tue, Jul 17, 2012 at 3:50 AM, Gerard Pujadas gerard.pujadas]*[gmail.com < owner-chemistry!^!ccl.net> wrote: > Dear CCL list members, > > first of all, sorry for cross-posting > > I would like to know if there is available any webserver (or software) > that can draws topological diagrams for PDB files following the idea that > was implemented some years ago at the TOPS webserver ( > http://www.tops.leeds.ac.uk/). This server is not running since 2008 and > it was quite useful in order to teach the protein architecture to my > students. Currently PDBSum provides topological diagrams for PDB entries ( > http://kpwu.wordpress.com/2006/02/14/pdbsum-announces-topology-diagrams-for-protein-domains/) > but, in my opinion, those formerly provided by TOPS where more intuitive to > correlate the diagram with the folding of the domain ... > > With many thanks in advances > > Yours sincerely > > -- > Gerard Pujadas > http://bioquimica.urv.cat/eng/fitxa.jsp?id=22 > Nutrigenomics Research Group > phone +34 977 55 (9565) > Biochemistry and Biotechnology Department > Office 106, Building N4, Campus Sescelades > Universitat Rovira i Virgili > Tarragona, Catalonia > > --f46d04071785d183e104c50b3cac Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable A quick Google search using "Tops protein server" found the follo= wing sites. The first is a new link to the new TOPS server at Glasgow. Hope= this helps you. Not all links on the home page are active. David

http://www.brc.dcs.= gla.ac.uk/projects/tops/

http://balabio.dcs.gla.ac.uk/drg/compare.html
http://www.bioinf.org.uk/tops= can/

http://fatcat.b= urnham.org/TOPS/

http://bioinformatics.burnham.org/pages/servers/

http:/= /www.biochem.ucl.ac.uk/~roman/links/index.html

On Tue, Jul 17, 2012 at 3:50 AM, Gerard Pujadas gerard.pujadas]*[= gmail.com <owner-chemistry!^!ccl.net<= /a>> wrote:
Dear CCL list members,

first of all, = sorry for cross-posting

I would like to know if there is available any webserver (or software)=20 that can draws topological diagrams for PDB files following the idea=20 that was implemented some years ago at the TOPS webserver (http://www.tops.leeds.ac.uk/= ). This server is not running since 2008 and it was quite useful in order to= =20 teach the protein architecture to my students. Currently PDBSum provides topological diagrams for PDB entries (http://kpwu.wordpress.com/2006/02/14/pdbsum-announces-topology-= diagrams-for-protein-domains/) but, in my opinion, those formerly provided by TOPS where more=20 intuitive to correlate the diagram with the folding of the domain ...

With many thanks in advances

Yours sincerely

--
G= erard Pujadas
http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22
Nutrigenomics Research Group
phone +34 977 55 (9565)
Biochemistry and Biotechnology Department
Office 106, Building N4, Campu= s Sescelades
Universitat Rovira i Virgili
Tarragona, Catalonia=


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