From mcblimts@leonis.nus.sg Tue May 6 00:41:08 1997 Received: from sable.nus.sg for mcblimts@leonis.nus.sg by www.ccl.net (8.8.3/950822.1) id AAA28148; Tue, 6 May 1997 00:28:26 -0400 (EDT) Received: from leonis.nus.sg (root@leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.8.4/8.6.9) with ESMTP id MAA30613 for ; Tue, 6 May 1997 12:28:15 +0800 (SST) Received: from limts.imcb.nus.sg ([137.132.42.122]) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) with SMTP id MAA10691 for ; Tue, 6 May 1997 12:28:13 +0800 Date: Tue, 6 May 1997 12:28:13 +0800 Message-Id: <199705060428.MAA10691@leonis.nus.sg> X-Sender: mcblimts@leonis.nus.sg X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Lim Teck Sin Subject: information on SDF format Hi, Does anyone know if the specification for SDF format is publicly available? Is there a site which document the various formats that have been widely used by chemists? Thanks! Best Regards Teck Sin From ccl@www.ccl.net Tue May 6 04:49:21 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id EAA01618; Tue, 6 May 1997 04:33:33 -0400 (EDT) Received: from faui45.informatik.uni-erlangen.de for model97@organik.uni-erlangen.de by bedrock.ccl.net (8.8.3/950822.1) id EAA15191; Tue, 6 May 1997 04:33:28 -0400 (EDT) Received: from derioc1.organik.uni-erlangen.de (derioc1.organik.uni-erlangen.de [131.188.128.1]) by uni-erlangen.de with SMTP id KAA16918 (8.7.6/7.5c-FAU); Tue, 6 May 1997 10:30:17 +0200 (MET DST) Received: from indigo11.organik.uni-erlangen.de (indigo11.organik.uni-erlangen.de [131.188.128.69]) by organik.uni-erlangen.de with SMTP id KAA08519 (8.6.12/7.4f-FAU);; Tue, 6 May 1997 10:29:03 +0200 Date: Tue, 6 May 1997 10:29:03 +0200 (MDT) From: "Modelling '97" To: chem-com@mailbase.ac.uk, chem-mod@mailbase.ac.uk, chemistry@ccl.net, ipmdg-l@venus.co.uk, amber@cgl.ucsf.edu, c2-l@msi.com, cache@pacificu.edu, charmm-bbs@emperor.harvard.edu, hyperchem@hyper.com, mmodinfo@uoft02.utoledo.edu, quanta-l@msi.com, sybyl@extreme.chem.rpi.edu, watoc@ic.ac.uk Subject: MGMS Bursaries : Model(l)ing '97 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The Molceular Graphics and Modelling Society (MGMS) is pleased to announce that it will be awarding a total of eight bursaries for young scientists for the Model(l)ing '97 conference in Erlangen, Germany, from 2-5 Sept. 1997. For details of the conference see: http://www.organik.uni-erlangen.de/model97 Bursaries will be awarded to graduate students or postdocs who give a lecture or present a poster at the conference. Note that the deadline for lecture submissions (originally May 1st) has been extended to June 1st to allow applications for bursaries. The deadline for poster submissions from bursary-applicants is also June 1st, not July 1st as for other posters. The bursaries will include conference regstration, accomodation in an economy room and a contribution towards travel expenses. Applications should be via the electronic registration facility availble through the above URL and should be accompanied by a recommendation from the supervisor emeiled to model97@organik.uni-erlangen.de Decisions as to the winners of the bursaries will be announced on June 1st. ----- Model(l)ing '97 Computer Chemie Centrum - Institut f. Organische Chemie I Naegelsbachstrasse 25 - D-91052 Erlangen Deutschland / Germany Tel: 0049-9131 - 85 6581 Fax: 0049-9131 - 85 6565 E-Mail: model97@organik.uni-erlangen.de WWW: http://www.organik.uni-erlangen.de/model97/ From beroza@scripps.edu Tue May 6 20:41:33 1997 Received: from relay.scripps.edu for beroza@scripps.edu by www.ccl.net (8.8.3/950822.1) id UAA01309; Tue, 6 May 1997 20:02:27 -0400 (EDT) Received: from euler.scripps.edu (euler.scripps.edu [137.131.252.34]) by relay.scripps.edu (8.8.5/TSRI-1.5) with ESMTP id RAA21955; Tue, 6 May 1997 17:02:20 -0700 (PDT) Received: (from beroza@localhost) by euler.scripps.edu (8.8.5/TSRI-1.4) id RAA05078; Tue, 6 May 1997 17:01:49 -0700 (PDT) Date: Tue, 6 May 1997 17:01:49 -0700 (PDT) From: Paul Beroza Message-Id: <199705070001.RAA05078@euler.scripps.edu> To: CHEMISTRY@www.ccl.net, Vladislav.Vassiliev@bri.nrc.ca Subject: Re: CCL:How to calculate pKa values in large proteins?... Dr. Vassiliev wrote: > > Let's imagine I have coordinates of a real protein (for example, from > PDB) and now I would like to know the pKa values of all the residues > (Asp's, Glu's, Lys's, Arg's, His's) at a given pH. What kind of programs > could predict these pKa values? > > I would also be interested in any references concerning the approaches of > this kind of prediction. > Several research groups have investigated this problem, commonly referred to as the "multiple site titration problem". The most widespread approach is to assume that the pKa of a titrating residue is perturbed from its solution value by the electrostatic environment it experiences in the protein. The electrostatic energies involved can be calculated from continuum models using finite difference, and other, numerical methods. I've appended a list of references dealing with the subject (liberally sprinkled with references to my own work, of course). There are many more. I think the Bashford and Karplus paper is a good place to start, though more recent work uses more sophisticated models. Alternatively, Arieh Warshel has a more microscopic PDLD model (protein dipoles langevin dipoles) which has also been applied to pKa calculation in proteins. Several available computer programs can do these sorts of calculations: MEAD (from Don Bashford ftp.scripps.edu:pub/bashford) pep (my finite difference code ftp.scripps.edu:pub/beroza) DELPHI (from Barry Honig's group) UHBD (from Andy McCammon's group) polaris (from Arieh Warshel's group) Hope this helps, Paul --------------------------------------------------------------- Paul Beroza, Ph.D. The Scripps Research Institute email: beroza@scripps.edu Department of Molecular Biology phone: 619-784-9957 10550 N. Torrey Pines Rd. - TPC15 fax: 619-784-8896 La Jolla, CA 92037 URL: www.scripps.edu/~beroza --------------------------------------------------------------- @ARTICLE{Russel, AUTHOR="S. T. Russel and A. Warshel", JOURNAL="J. Mol. Biol.", TITLE="The Energetics of Ionized Groups in Bovine Pancreatic Trypsin Inhibitor", VOLUME="185", PAGES="389-404", YEAR="1985" } @ARTICLE{Bashford90, AUTHOR="D. Bashford and M. Karplus", JOURNAL="Biochemistry", TITLE=" {${\rm pK_a}$'s} of Ionizable Groups in Proteins: Atomic Detail from a Continuum Model", VOLUME="29", PAGES="10219-10225", YEAR="1990" } AUTHOR="P. Beroza and D. R. Fredkin and M. Y. Okamura and G. Feher", JOURNAL="Proc. Natl. Aca. Sci.", TITLE="Protonation of Interacting Residues in a Protein by a {M}onte {C}arlo Method: {A}pplication to Lysozyme and the Photosynthetic Reaction Center of {{\it Rhodobacter sphaeroides}}", VOLUME="88", PAGES="5804-5808", YEAR="1991" } @ARTICLE{Oberoi93, AUTHOR="H. Oberoi and N. M. Allewell", JOURNAL="Biophys. J.", TITLE="Multigrid Solution of the Nonlinear Poisson-Boltzmann Equation and Calculation of Titration Curves", VOLUME="65", PAGES="48-55", YEAR="1993" } @ARTICLE{Yang93, AUTHOR="A.-S. Yang and M. R. Gunner and R. Sampogna and K. Sharp and B. Honig", JOURNAL="Proteins", TITLE="On the Calculation of {${\rm pK_a}$'s} in Proteins", VOLUME="15", PAGES="252-265", YEAR="1993" } @ARTICLE{Antosiewicz94, AUTHOR="J. Antosiewicz and J.A. McCammon and M.K. Gilson", TITLE="Prediction of pH-dependent Properties of Proteins", JOURNAL="J. Mol. Biol.", VOLUME="238", PAGES="415-436", YEAR="1994" } @ARTICLE{You95, AUTHOR="T.J. You and D. Bashford", TITLE="Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility", JOURNAL="Biophys. J.", VOLUME="69", PAGES="1721-1733", YEAR="1995" } @ARTICLE{Beroza95, AUTHOR="P. Beroza and D. R. Fredkin and M. Y. Okamura and G. Feher", JOURNAL="Biophys. J.", TITLE="Electrostatic Calculations of Amino Acid Titration and Electron Transfer, {${\rm Q_A^- Q_B \rightarrow Q_A Q_B^-}$}, in the Reaction Center", VOLUME="68", PAGES="2233-2250", YEAR="1995" } @ARTICLE{Beroza96, AUTHOR= "P. Beroza and D. R. Fredkin", TITLE="Calculation of Amino Acid {${\rm pK_a}$s} in a Protein from a Continuum Electrostatic Model: Method and Sensitivity Analysis", JOURNAL="J. Comp. Chem.", VOLUME="17", PAGES="1229-1244", YEAR="1996" } @ARTICLE{Beroza96, AUTHOR= "P. Beroza and D. A. Case", TITLE="Including Side Chain Flexibility in Continuum Electrostatic Calculations of Protein Titration", JOURNAL="J. Phys. Chem.", VOLUME="100", PAGES="20156-20163", YEAR="1996" }