From ccl@www.ccl.net Thu Dec 12 12:09:11 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA21530; Thu, 12 Dec 1996 11:57:30 -0500 (EST) Received: from UICVM.UIC.EDU for U54632@UICVM.UIC.EDU by bedrock.ccl.net (8.8.3/950822.1) id LAA17280; Thu, 12 Dec 1996 11:57:27 -0500 (EST) From: Message-Id: <199612121657.LAA17280@bedrock.ccl.net> Received: from UICVM.UIC.EDU by UICVM.UIC.EDU (IBM VM SMTP V2R2) with BSMTP id 0003; Thu, 12 Dec 96 10:57:27 CST Received: from UICVM (NJE origin U54632@UICVM) by UICVM.UIC.EDU (LMail V1.2a/1.8a) with BSMTP id 9373; Thu, 12 Dec 1996 10:57:24 -0600 Date: Thu, 12 Dec 1996 10:44:51 CST To: Subject: Crystal structure of trimethoprim bound to E. coli DHFR Dear CCLers: I would like to have the coordinates for the crystal structure of trimethoprim bound to E. coli DHFR. It is not available in the PDB. Any suggestions as to where I could find this information, would be highly appreciated. The crystal structure was solved in 1985, and the reference for it is: Mathews,D. A.; Bolin, J. T.; Burridge, J. M.; Filman, D. J.; Volz, K. W.; Kaufman, B. T.; Beddell, C. R>; Champness, J. N.; Stammers, D. K.; Kraut, J.; "Refined crystal structures of Escherichia coli and chicken liver dihydrofolate reductase containing bound trimethoprim" J. Biol. Chem., v 260, 381-391 (1985) If there is sufficient interest, I will summarize the responses for the net. Thanking you, Sincerely, Chaya Duraiswami (email: cdurai1@uic.edu) From polowin@hyper.hyper.com Thu Dec 12 12:12:30 1996 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.8.3/950822.1) id LAA21328; Thu, 12 Dec 1996 11:33:01 -0500 (EST) Received: from hyper.hyper.com (hyper.hyper.com [206.51.24.9]) by www.hyper.com (8.6.12/8.6.12) with SMTP id LAA00273; Thu, 12 Dec 1996 11:41:11 -0500 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:CHEMISTRY@www.ccl.net id AA00619; Thu, 12 Dec 96 11:37:26 -0500 Date: Thu, 12 Dec 96 11:37:26 -0500 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9612121637.AA00619@hyper.hyper.com> To: somsak@atc.atccu.chula.ac.th (Somsak Tonmunphean), CHEMISTRY@www.ccl.net Subject: Re: CCL:G:How to calculate Bond Order ? > From: somsak@atc.atccu.chula.ac.th (Somsak Tonmunphean) > Date: Thu, 12 Dec 1996 18:55:41 +0000 (WET) > > I am doing my thesis with the subject of QSAR of antimalarial > drugs. My available chemical calculation softwares are Gaussian 92, > Hyperchem release 3, ChemPlus, Alchemy, and Molgen. From some papers, > they calculated bond orders and found that these had good correlations > with activity so I would like to try it but unfortunately I really don't > know how to calculate the bond order of molecules. Does anybody know how > to do so (if possible with the programs I have) ? It is not possible to calculate bond orders automatically with HyperChem, but they can be calculated manually from the density matrices, which can be printed in a log file. The bond order between atoms A and B is the sum of the squares of the elements in the density matrix with rows for atom A's orbitals and columns for atom B's orbitals, or vice versa. If you are doing UHF calculations, you must add the elements of the alpha and beta matrices together before squaring. I tried this for C2H4 as model-built, with an AM1 single-point calculation, and got a C--C bond order of 2.0004. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From ccl@www.ccl.net Thu Dec 12 13:09:11 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA21914; Thu, 12 Dec 1996 12:56:43 -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 MAA19091; Thu, 12 Dec 1996 12:56:40 -0500 (EST) From: Received: from puccini.TechFak.Uni-Bielefeld.DE by techfac.TechFak.Uni-Bielefeld.DE id AA19660; Thu, 12 Dec 1996 18:55:56 +0100 Received: by puccini.TechFak.Uni-Bielefeld.DE (5.65/tp.29.08.90) id AA14702; Thu, 12 Dec 1996 18:55:55 +0100 Date: Thu, 12 Dec 1996 18:55:55 +0100 Message-Id: <9612121755.AA14702@puccini.TechFak.Uni-Bielefeld.DE> Apparently-To: chemistry@ccl.net 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 ccl@www.ccl.net Thu Dec 12 16:09:13 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA23065; Thu, 12 Dec 1996 15:43:11 -0500 (EST) Received: from mailhub.Stanford.EDU for holbrook@SMI.Stanford.EDU by bedrock.ccl.net (8.8.3/950822.1) id PAA27532; Thu, 12 Dec 1996 15:43:08 -0500 (EST) Received: from [171.65.84.228] (smrl-fp-dynamic-228.Stanford.EDU [171.65.84.228]) by mailhub.Stanford.EDU (8.7.5/8.7.3) with SMTP id MAA00923; Thu, 12 Dec 1996 12:43:06 -0800 (PST) Date: Thu, 12 Dec 1996 12:43:06 -0800 (PST) X-Sender: holbrook@camis.stanford.edu (Unverified) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net, biotech@umdc.umd.edu, binglis@ufthm.health.ufl.edu, marian@micro.ifas.ufl.edu, letter@NMRSG.MMRRCC.UPENN.EDU From: holbrook@SMI.Stanford.EDU (Robin Holbrook) Subject: NATO ASI on Protein Dynamics, Function and Design in April '97 Could you please list our upcoming Advanced NMR Study Insitute on your Calendar/List of Meetings. The URL for more information and registration is: http://cmgm.stanford.edu/SMRL/Erice97.html And the basic info is: International School of Structural Biology and Magnetic Resonance 3rd Course: Protein Dynamics, Function and Design April 16-28, 1997 Directors: Jean-Francois Lefevre and Oleg Jardetzky to be held at the Ettore Majorana Centre for Scientific Culture Erice, Sicily, Italy. For more information or to apply to attend contact Robin Holbrook holbrook@smi.stanford.edu Tel: 415/723-6270 Fax: 415/723-2253 Robin Holbrook Stanford Magnetic Resonance Laboratory Stanford University Stanford, CA 94305-5055 Tel: 415/723-6270 Fax: 415/723-2253 From ccl@www.ccl.net Thu Dec 12 17:09:13 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id QAA23363; Thu, 12 Dec 1996 16:45:33 -0500 (EST) Received: from UMSLVMA.UMSL.EDU for wwelsh@jinx.umsl.edu by bedrock.ccl.net (8.8.3/950822.1) id QAA28979; Thu, 12 Dec 1996 16:45:32 -0500 (EST) Received: from admiral.umsl.edu by UMSLVMA.UMSL.EDU (IBM VM SMTP V2R2) with TCP; Thu, 12 Dec 96 15:45:28 CST Received: from chewwels.umsl.edu by admiral.umsl.edu (SMI-8.6) id PAA15680; Thu, 12 Dec 1996 15:45:24 -0600 Date: Thu, 12 Dec 1996 15:45:24 -0600 Message-Id: <199612122145.PAA15680@admiral.umsl.edu> X-Sender: wwelsh@jinx.umsl.edu X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: William Welsh Subject: Email Address Dear Netters, Can someone give me the email address for Jim Damewood at Seneca? Thanks ... Bill Welsh