From FS300627@Sol.YorkU.CA Sun Jan 29 11:40:40 1995 Received: from Sol.YorkU.CA for FS300627@Sol.YorkU.CA by www.ccl.net (8.6.9/930601.1506) id LAA20294; Sun, 29 Jan 1995 11:09:50 -0500 From: Received: from Sol.YorkU.CA by Sol.YorkU.CA (PMDF V4.3-7 #6007) id <01HMF0AS140G8WWNWW@Sol.YorkU.CA>; Sun, 29 Jan 1995 11:09:43 EST Date: Sun, 29 Jan 1995 11:09:43 -0500 (EST) Subject: 3D Net search summary and additional questions To: chemistry@ccl.net Message-id: <01HMF0AS2ZJ68WWNWW@Sol.YorkU.CA> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Greetings, As promissed, I have included a summary of responses to my question about internet 3D searches. The summary (attached at the end of this message) only contains responses that actually gave some information. Most of the responses I got were:'please summerize' I have however, some additional questions before I post the summary. >From the responses it is clear that there are very little databases that can be searched from a remote site. This I find a bit surprizing since I believe that the technology is there. Now I can think of several possible reasons why there are so little remote sites but I am interested in what other people think of it. Here are some of the reasons I could think of: - Security risks. Sending files of molecules that are potential drugs over the Internet might not be very safe. This could however be avoided perhaps by sending files per courier to the remote site. - Profits. Companies that sell large databases would rather sell one at several thousand $$ than having to charge much less on a per search basis. - Technology. To send compounds that have been modelled to represent the (believed) minimum energy structure over the Net is not possible. I do not know. I have not tried it yet. - Payment methods. Methods to pay for services over the Net is still not perfect and we'll have to wait until this is perfected. (but what about credit cards?) The reason I am interested in remote site database searches is because BioMimic feels that there is a place for 'out-house' molecular modelling. However, to invest in several large databases is too expensive and therefore the question about structure searches from a remote site. One last question before I post the summary. My question was directed to 3D searches and since the response was minimal, does anyone know about 2D 'remote' searches? Patrick ************************************************************************** ** Patrick van der Valk M.Sc. | It is a capital mistake to theorize * ** BioMimic | before one has data. Insensibly one * ** | begins to twist facts to suit theories * ** e-mail:FS300627@Sol.YorkU.Ca | instead of theories to suit facts. * ** Phone: (416) 736-5747 | * ** Fax: (416) 650-3558 | -Sherlock Holmes- * ************************************************************************** --------------------------------------------------------------------------- From:IN%"carlos@extreme.bio.cornell.edu" To:IN%"FS300627@Sol.YorkU.CA" CC:IN%"carlos@extreme.bio.cornell.edu" Subj:Cambridge Structural Database at CISTI, NRC Patrick, IIbelieve that people at CISTI, NRC Ottawa would be all too happy to charge you to carry out a search. Their number is (613)993-1600 You can ask to speak to either: Dr. Roger Gough or Dr. John Rogdgers they both know how to run a search in this database. If I can be of further help please let me know By the way what is 'Biomimic'? Carlos ------------------------------------------------------------------------- From:IN%"ccl@ccl.net" "Computational Chemistry" To:IN%"FS300627@Sol.YorkU.CA" CC: Subj:RE: CCL:Structure searches though the Interne - Reply I would be interested in a summary. There are cystallagraphic databases available at CAN/SND for a fee. Send a note to CANSND@INFO.CISTI.NRC.CA for more info. ------------------------------------------------------------------------ From:IN%"bkarlak@ren.onyx-pharm.com" "Brian Karlak" To:IN%"FS300627@Sol.YorkU.CA" CC: Subj:RE: CCL:Structure searches though the Internet You might want to contact Daylight software in New Mexico, USA at (505)989-1000. Last I heard, they had a service called Mjollnir (it's the name of Thor's hammer) that allowed remote database searches. I don't know if it's 3-D or not. Brian Karlak Computational Chemist Onyx Pharmaceuticals "Update all information. Pod into cosmos." Jeffffff aid it. i believe it. That settles it. ----------------------------------------------------------------------- From san@mbu.iisc.ernet.in Sun Jan 29 12:40:42 1995 Received: from sangam.ncst.ernet.in for san@mbu.iisc.ernet.in by www.ccl.net (8.6.9/930601.1506) id MAA20720; Sun, 29 Jan 1995 12:36:18 -0500 From: Received: from iisc.ernet.in (iisc.iisc.ernet.in [144.16.64.3]) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with SMTP id XAA16872 for ; Sun, 29 Jan 1995 23:05:42 +0530 Received: from vigyan.UUCP by iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA14375; Sun, 29 Jan 95 23:10:49+0530 Date: Sun, 29 Jan 95 23:10:49+0530 Message-Id: <9501291740.AA14375@iisc.ernet.in> Received: by vigyan.iisc.ernet.in (smail2.3) id AA18841; 29 Jan 95 23:05:08 EST (Sun) To: vigyan!chemistry@ccl.net Subject: data analysis of large biomolecules Hi! I am doing statistical analysis of the PDB crystal structures of proteins. I would like to know what all are the methods in vogue of such purposes and more importantly I would like to hear from the experienced people about the use of such approaches in gaining biological and structural/sequence insights for proteins and its practical uses apart from prediction. I know a lot of litrature exists on this, but what I am looking for is the first hand advice from the people about the difficulties they face in undertaking such projects. Of course, a list of general references about it is a welcome. I am more interested in analyzing protein secondary structures e.g. helices. Their shapes (say curved or linear), their packing etc. and trying to correlate with their sequences. So please respond in this spirit only. I shall summarize to the net. yours' cordially sandeep kumar san@mbu.iisc.ernet.in From bruce@cosy.utmb.edu Sun Jan 29 13:40:40 1995 Received: from cosy.utmb.edu for bruce@cosy.utmb.edu by www.ccl.net (8.6.9/930601.1506) id NAA20973; Sun, 29 Jan 1995 13:14:22 -0500 Received: by cosy.utmb.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA10195; Sun, 29 Jan 95 12:19:02 -0600 Date: Sun, 29 Jan 95 12:19:02 -0600 From: bruce@cosy.utmb.edu (Bruce A. Luxon) Message-Id: <9501291819.AA10195@cosy.utmb.edu> To: chemistry@ccl.net Subject: WWW Oversight I've enjoyed the discussion on Chem WWW lists et al but my $.02 is that some have missed an essential point. That is that there is a strong element of personal initiative and free enterprise on setting up WWW sites and maintaining them and this is good. I did mine when I had about 2 weeks of slack time. I had no idea what I was getting in to but it was interesting and kind of fun. My associates find that it is a useful place to launch their internet meanderings - thus it is successful. As a rule my time is taken up with research/meetings/writing papers & grants/etc and other forms of making a living so my WWW pages sort of come when I don't have anything else to do or I just need a break. I suspect many others are in the same boat. This explains the lack of graphics in my WWW server. My stuff is continually in transition and I hope getting better (ie more useful to those who use it). The idea that some self appointed committee is going to referee the quality of my web site is abhorent. If you don't like a particular site don't visit it anymore. We don't need anymore control freaks than we already have. Bruce *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* * Bruce A. Luxon, Ph.D * * Assistant Professor U * Dept. of Human Biological Chemistry & Genetics T * University of Texas Medical Branch M * Galveston, TX 77555-1157 B * * * (409)747-6802; Fax (409)747-6850 * * bruce@nmr.utmb.edu http://www.nmr.utmb.edu/ * *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-* From alex@mmiris.ab.umd.edu Sun Jan 29 14:40:41 1995 Received: from comm1.ab.umd.edu for alex@mmiris.ab.umd.edu by www.ccl.net (8.6.9/930601.1506) id OAA21617; Sun, 29 Jan 1995 14:39:33 -0500 From: Received: by comm1.ab.umd.edu (5.65/DEC-Ultrix/4.3) id AA00746; Sun, 29 Jan 1995 14:39:31 -0500 Received: by mmiris.ab.umd.edu (931110.SGI/911001.SGI) for @comm1.ab.umd.edu:chemistry@ccl.net id AA16456; Sun, 29 Jan 95 14:52:18 -0500 Date: Sun, 29 Jan 95 14:52:18 -0500 Message-Id: <9501291952.AA16456@mmiris.ab.umd.edu> To: MARLA@chemf.rutgers.edu Cc: chemistry@ccl.net In-Reply-To: Marla Babcock's message of Mon, 6 Jun 94 15:50 EST <0723C5628BFF601AAC@chemf.rutgers.edu> Subject: CCL:Nucl Acid Struct Analysis Prog Release Dr. Babcock Would it be possible to obtain copies of your code(s) for the analysis if nucleic acid structures? Thank you. Alex MacKerell, alex@mmiris.ab.umd.edu School of Pharmacy University of Maryland at Baltimore 20 North Pine Street Baltimore, MD 21201 410-706-7442