From chemistry-request*- at -*server.ccl.net Mon Oct 23 14:28:33 2000 Received: from stillwater.cs.umt.edu (stillwater.cs.umt.edu [150.131.15.39]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA31101 for ; Mon, 23 Oct 2000 14:28:32 -0400 Received: from [150.131.15.54] (dakota.cs.umt.edu [150.131.15.54]) by stillwater.cs.umt.edu (8.9.3+Sun/8.9.3) with ESMTP id MAA08316 for ; Mon, 23 Oct 2000 12:28:18 -0600 (MDT) User-Agent: Microsoft Outlook Express Macintosh Edition - 5.01 (1630) Date: Mon, 23 Oct 2000 12:42:11 -0600 Subject: RE: programs for generation of topological indices From: "Clair W. Cabal" To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit I have received a couple of requests to share the information I received in responses to my query. Thank you very much to those who took the time to send me information. My original message is followed by a summary of the responses: Date: Mon, 16 Oct 2000 13:04:01 -0600 (MDT) From: Clair W Cabal To: chemistry[ AT ]ccl.net Subject: programs for generation of topological indices All, Please forgive me if this is a redundant request, but in reviewing the archives, I don't see much on this topic since 1995. I am in search of a stand alone program to generate a very large number of toplogical indices for chemical compounds. I know of, but am not familiar with MOLCONN-X, QuaSar-Descriptor and Dr. Basak's POLLY 2.3. A respondent to this query posed in 1995 mentioned a program called EMMA which could handle up to 2,000 descriptors, but I have not received a response to an inquiry about this from the developer at Moscow State University. I would appreciate any feedback about use of the above mentioned programs and any information about others that may have been developed more recently. Thank you. Clair Cabal Research Assistant Machine Learning Research Lab Department of Computer Science University of Montana Missoula, Montana email: cabal&$at$&cs.umt.edu fax: (406) 243-5139 --------------------------------------------------------------------------- Date: Tue, 17 Oct 2000 08:58:58 From: "Rob Williams" To: "'Clair W Cabal'" Subject: RE: programs for generation of topological indices Hi Clair, Oxford Molecular distributes a product called TsarBatch. It is a stand-alone version of the descriptor generation parts of their Tsar QSAR product. I wasn't sure from your e-mail whether you were after a program that calculates a very large range of descriptors, or one that calculates standard topological indices for a very large number of structures. TsarBatch is more in the latter of these two categories. You can find more information at: http://www.oxmol.com/software/tsarbatch/ There is a fact sheet that you can download from there. Hope this is of interest to you. Best regards, Rob ------------------------------ Date: Tue, 17 Oct 2000 07:30:06 From: Doug Henry To: "'cabal # - at - # cs.umt.edu'" Subject: FW: programs for generation of topological indices The Dragon program was recently posted. It takes Sybyl Mol2 and Hyperchem hin files, and can generate 800+ descriptors. It can be used in conjunction with Babel, but I found the resulting files must have extra blanks removed from the files to be acceptable to Dragon. It can take a directory of molecule files, generate a file with descriptor values, then allows you to add your own "Y" colums to the data: Dear Colleague, We would like to advertise that the new software DRAGON (version 1.0) for the calculation of 853 theoretical molecular descriptors is now free downloadable from our Website. This software has been produced by us, coherently to the Handbook of Molecular Descriptors, by Roberto Todeschini and Viviana Consonni, edited in these days by WILEY - VCH, in the Series of Methods and Principles in Medicinal Chemistry, Vol. 11 (Editors: R.Mannhold, H.Kubinyi, H.Timmerman); pp.680. We have also activated a bibliographic reference service about molecular descriptors at our Website and a special e-mail address (moldes {*at*} disat.unimib.it) for the exchange of information of the researchers in this field. Best regards, Roberto Todeschini and Viviana Consonni ---------------------------------------------------------------------------- -------- Milano Chemometrics and QSAR Research Group Department of Environmental Sciences P.za della Scienza, 1 - 20126 Milano (italy) WebSite: http://www.disat.unimib.it/chm/ Dough ^at^ mdli.com (just a user) ------------------------------ Date: Wed, 18 Oct 2000 11:38:07 From: "Vladimir A. Palyulin" To: cabal: at :cs.umt.edu Subject: descriptors Dear Clair Cabal, Just a few days ago Milano Chemometrics group headed by Professor Roberto Todeschini released free version of DRAGON program which computes about 850 descriptors. It can be downloaded from: http://www.disat.unimib.it/chm/ Sincerely, Vladimir Palyulin, Head, Group of Computer Molecular Design, Department of Chemistry, Moscow State University P.S. EMMA program was oriented for DOS and was developed in 1988-1993, now we are working on Windows program which computes thousands descriptors, which are treated with neural networks. ------------------------------ Thanks also to Elena Fioravanzo for forwarding information about DRAGON. I should mention that DRAGON does not just produce topological indices, but generates 14 classes of theoretic descriptors including geometric, information theoretic, constitutional and BCUT descriptors to name a few. I have run some test data with DRAGON and find it to be very easy to use. Now my task is to convert existing data into mol file format! Clair Cabal