From MAILER-DAEMON@www.ccl.net Wed Sep 6 13:41:57 1995 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.6.10/950822.1) id NAA25900; Wed, 6 Sep 1995 13:41:01 -0400 Received: by schiele (950215.SGI.8.6.10/940406.SGI.AUTO) for chemistry@www.ccl.net id TAA01279; Wed, 6 Sep 1995 19:40:26 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9509061940.ZM1277@schiele> Date: Wed, 6 Sep 1995 19:40:18 -0600 Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: chemistry@www.ccl.net Subject: CCL:Java chemistry applets? Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Status: RO On Sep 6, 10:06, Hinsen Konrad wrote: > Subject: CCL:Java chemistry applets? > > Sun has been promoting a new programming language, java, as a tool > for creating portable applications on internet. Instead of constantly > going back to the host for additional information (a response to a mouse > click, for example), the applet executes on the local client. > > And others have had similar ideas, as always... There is a beta test > version of a new Web browser called Grail, which uses Python as its > programming language for such applets. Look at > http://monty.cnri.reston.va.us/grail/ > for details. > >-- End of excerpt from Hinsen Konrad Not enough. There is also CandleWeb (using a language pronounced 'awe' and written Å (A with circle on top, in case your mail reader cannot display ISO-characters) http://www.oslonett.no/~candle/ and a recently announced new tcl/tk-based WWW browser (not tkWWW, but I lost the reference) which uses "secure tcl", a controlled execution environment for tcl and tk to execute applet code, and I use (not yet secure) tcl/tk for my apps ... http://schiele.organik.uni-erlangen/cactvs/scripts.html -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From arthur@csb0.IPC.PKU.EDU.CN Sat Sep 9 21:51:34 1995 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/950822.1) id VAA26782; Sat, 9 Sep 1995 21:48:04 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA07009; Sun, 10 Sep 95 09:34:19 -0700 Date: Sun, 10 Sep 1995 09:34:18 -0700 (PDT) From: Arthur Wang To: CCL mailing list Subject: Summary of Calculation of LogP Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: R Hello, everyone! Last week I put forward the query for references of calculation of LogP and I got a few of very helpful answers. I should thank all who have given their kind hands. Here is the summary. Regards, Arthur Wang +===========================================================+ | | | Arthur Wang Doctoral Candidate | | | | Molecular Design Lab | | Institute of Physical Chemistry, Peking University | | Beijing 100871, P.R.China | | | | E-mail: arthur@ipc.pku.edu.cn | | Tel: 86-10-2501490 Fax: 86-10-2501725 | | WWW: http://www.ipc.pku.edu.cn/arthur/homepage.html | | | +===========================================================+ ************************SUMMARY OF CALCULATION OF LOGP*********************** Piece One: ----------------------------------------------------------------------------- From: vis@gensia.com In response to your enquiry: There have been two recent comparisons of available methods. (i) Viswanadhan et al, J. Comp. Chem. (1993) 14, 1019-1026. (ii) Moriguchi, I., et al Chem. Pharm. Bull., (1994), 42, 976. A critique of the second review has also been published. Leo, A. J., Chem. and Pharm. Bull., (1995), 43, 512. After the pioneering work of Hansch and Leo on substituent constants for 'Log P' (or lipophilicity), there have been several atttempts to develop methods simpler (such as the use of 'atomic' fragments, pioneered by Ghose and Crippen) and more complex (using information from Quantum Chemical calculations, such as the BLOGP method developed by N. Bodor and associates). Rekker's work on lipophilicity is highly notable as well. References for all these works may be found in the two references given above. We have developed the 'atomic' method much further, which is as yet unpublished. I believe several software companies are also developing newer versions & approaches and I am sure you will hear from them. ----------------------------------------------------------------------------- Piece Two: ----------------------------------------------------------------------------- From: jordi@stark.udg.es (Jordi Mestres) Here you will find enclosed some references on the calculation of Molecular Lipophilicity Potentials based on the atomic partition of the total molecular LogP contribution. Sincerely, Jordi -------------------------------------------------------------------------- 1 Ghose, A.K. and Crippen, G.M., J. Comput. Chem. 9 (1988) 80. 2 Furet, P., Sele, A. and Cohen, N.C., J. Mol. Graph. 6 (1988) 182. 3 Viswanadhan, V.N., Ghose, A.K., Revankar, G.R. and Robins, R.K., J. Chem. Inf. Comput. Sci. 29 (1989) 163. 4 Croizet, P., Langlois, M.H., Dubost, J.P., Braquet, P., Audry, E., Dallet, Ph. and Colleter, J.C., J. Mol. Graph. 8 (1990) 153. 5 Kantola, A., Villar, H.O. and Loew, G.H., J. Comput. Chem. 12 (1991) 681. 6 Heiden, W., Moeckel, G. and Brickmann, J. J. Comput.-Aided Mol. Design 7 (1993) 503. 7 Gaillard, P., Carrupt, P.-A., Testa, B. and Boudon, A., J. Comput.-Aided Mol. Design 8 (1994) 83. 8 Rozas, I., Du, Q. and Arteca, G.A., J. Mol. Graph. 13 (1995) 98. 9 Kurochkina, N. and Lee, B., Protein Engineering 8 (1995) 437. 10 Bone, R.G.A. and Villar, H.O., J. Mol. Graph. 13 (1995) 201. -------------------------------------------------------------------------- -------------------------------------------------------------------------- Piece Three ------------------------------------------------------------------------------ From: doyle@gibbs.oit.unc.edu (Donald Doyle) This was recently reviewed by Albert J. Leo. See Chem. Rev. vol.93, pp1281-1306 (June, 1993). ------------------------------------------------------------------------------ Piece Four ------------------------------------------------------------------------------ From: "Konrad, IRBM Chemistry, +39-6-91093606" Below is a list of log P refs which I have in my database. See chapters 4-5 in reference #13 for a good review of log P calculation methods. I you find these references useful and best of luck to you in developing your log P prediction method. (1) Dearden, J. C.; Bresnen, G. M. The measurement of partition coefficients. Quant. Struct.-Act. Relat. 1988, 7, 133-144. (2) Essex, J. W.; Reynodls, C. A.; Richards, W. G. Theoretical determination of partition coefficients. J. Am. Chem. Soc. 1992, 114, 3634-3639. (3) Ghose, A. K.; Pritchett, A.; Crippen, G. M. Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships III: modelng hydrophobic interactions. J. Comput. Chem. 1988, 9, 80-90. (4) Koehler, M. G.; Grigoras, S.; Dunn, W. J., III The relationship between chemical structure and the logarithm of the partition coefficient. Quant. Struct.-Act. Relat. 1988, 7, 150-159. (5) Moriguchi, I.; Hirono, S.; Liu, Q.; Nakagome, I.; Matsushita, Y. Simple method of calculating octano/water partition coefficient. Chem. Pharm. Bull. 1992, 40, 127-130. (6) Moriguchi, I.; Hirono, S.; Nakagome, I.; Hirano, H. Comparison of reliability of log P values for drugs calculated by several methods. Chem. Pharm. Bull. 1994, 42, 976-978. (7) Richards, N. G. J.; Williams, P. B.; Tute, M. S. Empirical methods for computing molecular partition coefficients. I. Upon the need to model the specific hydration of polar groups in fragement-based approaches. Int. J. Quantum Chem.: Quantum Biology Symposium 1991, 18, 299-316. (8) (8) Richards, N. G. J.; Williams, P. B.; Tute, M. S. Empirical methods of computing molecular partition coefficients: II. Inclusion of conformational flexibility within fragment-based approaches. Int. J. Quantum Chem. 1992, 44, 219-233. (9) Viswanadhan, V. N.; Reddy, M. R.; Bacquet, R. J.; Erion, M. D. Assessment of methods used for predicting lipophilicity: application to nuceolsides and nuceloside bases. J. Comput. Chem. 1993, 14, 1019-1026. (10) Bodor, N.; Gabanyi, Z.; Wong, C.-K. A new method for the estimation of partition coefficient. J. Am. Chem. Soc. 1989, 111, 3783-3786. (11) Bodor, N.; Huang, M.-J. Predicting parition coefficients for isomeric diastereoisomers of some tripeptide analogs. J. Comput. Chem. 1991, 12, 1182-1186. (13) Hansch, C.; Leo, A. Exploring QSAR: Fundamentals and Applications in Chemistry and Biology; American Chemical Society: Washington, DC, 1995. ------------------------------------------------------------------------------ Piece Five: ------------------------------------------------------------------------------ From: MARTIN@cmda.abbott.com I'll just send some names, probably you have seen the articles: Leo, Al; Rekker; Ghose & Crippen; Moriguchi; Klopmann; Brinkman--JCICS recently; maybe unpublished but the QM people doing solvation test their model on logP--C. Cramer, Klampt (COSMO program), Tim Clark; I hear that the Wavefront people have a model; Darvas in a CompuChem module; . . . ------------------------------------------------------------------------------ ******************************THE END****************************************