From ccl@www.ccl.net Fri Dec 13 04:09:20 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id DAA26358; Fri, 13 Dec 1996 03:53:59 -0500 (EST) Received: from techfac.TechFak.Uni-Bielefeld.DE for friedric@TechFak.Uni-Bielefeld.DE by bedrock.ccl.net (8.8.3/950822.1) id DAA05643; Fri, 13 Dec 1996 03:52:49 -0500 (EST) Received: from puccini.TechFak.Uni-Bielefeld.DE by techfac.TechFak.Uni-Bielefeld.DE id AA28205; Fri, 13 Dec 1996 09:52:18 +0100 Received: by puccini.TechFak.Uni-Bielefeld.DE (5.65/tp.29.08.90) id AA06948; Fri, 13 Dec 1996 09:52:18 +0100 Message-Id: <9612130852.AA06948@puccini.TechFak.Uni-Bielefeld.DE> Subject: docking blind test To: chemistry@ccl.net Date: Fri, 13 Dec 1996 09:52:17 +0100 (GMT) From: Friedrich Ackermann X-Mailer: ELM [version 2.4 PL25] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear netters, in a pair of recently published articles the results of a blind test of PROTEIN DOCKING ALGORITHMS were published: @article{stryn96, author = {Strynadka, N. C. J. and Eisenstein, M. and Katchalski--Katzir, E. and Shoichet, B. K. and Kuntz, I. D. and Abagyan, R. and Totrov, M. and Janin, J. and Cherfils, J. and Zimmerman, F. and Olson, A. and Duncan, B. and Rao, M. and Jackson, R. and Sternberg, M. and James, M. N. G.}, title = {Molecular docking programs successfully predict the binding of a $\beta$--lactamase inhibitory protein to TEM--1 $\beta$--lactamase}, journal = {Nature Structural Biology}, year = {1996}, volume = {3}, pages = {233-239}} @article{shoic96, author = {Shoichet, B. K. and Kuntz, I. D.}, title = {Predicting the structure of protein complexes: a step in the right direction}, journal = {Chemistry \& Biology}, year = {1996}, volume = {3}, pages = {151-156}} The paper reporting on the discussed protein complex itself was @article{stryn96a, author = {Strynadka, N. C. J. and Jensen, S. E. and Alzari, P. M. and James, M. N. G.}, title = {A potent new mode of $\beta$--lactamase inhibition revealed by the 1.7{\AA} X--ray crystallographic structure of the TEM--1--BLIP complex}, journal = {Nature Structural Biology}, year = {1996}, volume = {3}, pages = {290-297}} My questions are: - Are the structures discussed in these papers already deposited in the PDB? - What are the relevant PDB-Id codes? I was able to extract some lactamase related PDB-entries, but I'm not sure whether they are the structures discussed in the papers quoted above. Any hint is appreciated! Best wishes, Friedrich Ackermann ------------------------------------------- Friedrich Ackermann Technical Faculty Applied Computer Science Bielefeld University P.O. 100131 D-33501 Bielefeld Phone: +49 521 106 2938 (2935) Fax: +49 521 106 2992 email: friedric@techfak.uni-bielefeld.de http://www.TechFak.Uni-Bielefeld.DE/techfak/persons/friedric/ ------------------------------------------- From nick@cherwell.com Fri Dec 13 12:09:24 1996 Received: from duct.mail.pipex.net for nick@cherwell.com by www.ccl.net (8.8.3/950822.1) id MAA29128; Fri, 13 Dec 1996 12:06:04 -0500 (EST) Received: from cherwell.com by duct.mail.pipex.net with SMTP (PP); Fri, 13 Dec 1996 17:06:03 +0000 Received: from mersey.cherwell.com by cherwell.com (4.1/SMI-4.1) id AA18475; Fri, 13 Dec 96 17:06:13 GMT Message-Id: <1.5.4.32.19961213170526.006d8224@cherwell.com> X-Sender: nick@cherwell.com X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 13 Dec 1996 17:05:26 +0000 To: chemistry@www.ccl.net From: Nick Lynch Subject: Re: CCL:M:Molecular Visualization on SUNs Hi CCLers, > However, I also need a program that will enable >us to build and visualize small molecules. We are developing a Java based program for the rendering and display of chemical structures on the web and within a Java enviroment. Running the Java SDK would enable you to run ChemSymphony locally and also to design web pages which allowed others to view structures within their Java compatible browsers. Further information is available from http://www.cherwell.com/cherwell Best wishes Nick --- --- Nick Lynch PhD | e-mail: nick@cherwell.com Commissioning Editor | Phone: +44 (0)1865 784812 Cherwell Scientific Publishing | Fax: +44 (0)1865 784801 Oxford OX4 4GA, UK | http://www.cherwell.com/cherwell --- ---