From chemistry-request@ccl.net Thu Apr 29 03:54:17 2004 Received: from collapsed.wormhole.hu (collapsed.wormhole.hu [195.70.35.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3T8sGkh002164 for ; Thu, 29 Apr 2004 03:54:16 -0500 Received: from ta1.sednet.hu ([212.97.0.169] helo=Moon) by collapsed.wormhole.hu with asmtp (Exim 3.36 #1 (Debian)) id 1BJ7K6-000199-00; Thu, 29 Apr 2004 10:55:14 +0200 Received: from szilva by Moon with local (Exim 3.36 #1 (Debian)) id 1BJ7GO-0000Jp-00; Thu, 29 Apr 2004 10:51:24 +0200 Date: Thu, 29 Apr 2004 10:51:24 +0200 From: Szilveszter Juhos To: Tom Halgren , chemistry$at$ccl.net Subject: CCL:Validating docking codes Message-ID: <20040429085124.GC543$at$computer.org> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.5.5.1+cvs20040105i Sender: Szilveszter Juhos X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Wed, Apr 28, 2004 at 05:56:08PM -0400, Tom Halgren wrote: [a lot of things to clear the database question concerning Glide] Sorry for my mistake and thank you very much for the precise answer (I even messed up ACD with ACS). Indeed it is the "Rognan set" I was writing about as that is the only set I am aware used by many different groups. I do not want to question the validation of Glide but want to point the lack of a common, freely available, drug/lead-like decoy set that would ease the comparison of different docking software. Cheers: Szilva From chemistry-request@ccl.net Thu Apr 29 02:47:14 2004 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3T7lCkh032497 for ; Thu, 29 Apr 2004 02:47:13 -0500 Received: from ac12.sci.kun.nl [131.174.179.19] (helo=ac12.sci.kun.nl) by wn1.sci.kun.nl (8.12.10/3.67) with ESMTP id i3T7mUFv025935; Thu, 29 Apr 2004 09:48:30 +0200 (MEST) From: "E.L. Willighagen" Reply-To: egonw*at*sci.kun.nl To: Miguel Romero , chemistry*at*ccl.net Subject: Re: CCL:FREE SOFTWARE Date: Thu, 29 Apr 2004 09:48:27 +0200 User-Agent: KMail/1.5.4 References: <40901E88.5060709*at*alumni.unav.es> In-Reply-To: <40901E88.5060709*at*alumni.unav.es> Cc: "Miguel" MIME-Version: 1.0 Content-Type: Text/Plain; charset="iso-8859-1" Content-Description: clearsigned data Content-Disposition: inline Message-Id: <200404290948.29279.egonw*at*sci.kun.nl> X-Spam-Status: No, hits=0.1 required=7.5 tests=SUBJ_FREE_CAP autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i3T7lEkh032501 -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Wednesday 28 April 2004 23:13, Miguel Romero wrote: > This is the first time I write to the CCL. I am starting a new molecular > modeling project in a new research group. I've used comercial modeling > software for many time but now I have to switch to something else, > preferably a FREE or reasonably priced software. I > > I am going to work with ligand-protein complexes and I need manipulation > software, doking and molecular mechanics (geometry optimization and > molecular dynamics) software. It can work under linux or windows sistems. > > Can anybody help me. > thanks in advance for any help! I'm not sure which programming language you plan to use (I guess C, C++ or even fortran...), but for visualization I do recommend Jmol (http://www.jmol.org) which is open source and has a very good 3D visualization of proteins which is even being improved every day by an international group of programmers and users. And since Java can easily bind to C/C++ code, it is quite straightforward to combine it with your code. I hope this helps, Egon - -- egonw*at*sci.kun.nl PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAkLNLd9R8I9Yza6YRApKhAJ9RnqwR+5tOQtMi05njsupTtKp4bQCfU/cK JWlUrnHYQ3UqB5hN60YpSbg= =UfX1 -----END PGP SIGNATURE----- From chemistry-request@ccl.net Thu Apr 29 10:15:33 2004 Received: from rwcrmhc12.comcast.net (rwcrmhc12.comcast.net [216.148.227.85]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3TFFWkh019912 for ; Thu, 29 Apr 2004 10:15:32 -0500 Received: from planaria (c-24-18-175-184.client.comcast.net[24.18.175.184]) by comcast.net (rwcrmhc12) with SMTP id <2004042915165901400d1l24e>; Thu, 29 Apr 2004 15:16:59 +0000 Reply-To: From: "Mark Thompson" To: "Miguel Romero" , Subject: RE: FREE SOFTWARE Date: Thu, 29 Apr 2004 08:16:52 -0700 Message-ID: <000701c42dfd$00367040$0200a8c0@planaria> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal In-Reply-To: <40901E88.5060709.-at-.alumni.unav.es> X-Spam-Status: No, hits=0.6 required=7.5 tests=SUBJ_ALL_CAPS,SUBJ_FREE_CAP autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Miguel, ArgusLab is free for academics. http://www.arguslab.com Runs on Windows (for now....) Mark *************************** Mark Thompson Planaria Software PO Box 55207 Seattle, WA 98155 voice: 206.240.4769 FAX: 206.440.3305 mark.-at-.arguslab.com http://www.arguslab.com *************************** -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request.-at-.ccl.net]On Behalf Of Miguel Romero Sent: Wednesday, April 28, 2004 2:14 PM To: chemistry.-at-.ccl.net Subject: CCL:FREE SOFTWARE Dear all, This is the first time I write to the CCL. I am starting a new molecular modeling project in a new research group. I've used comercial modeling software for many time but now I have to switch to something else, preferably a FREE or reasonably priced software. I I am going to work with ligand-protein complexes and I need manipulation software, doking and molecular mechanics (geometry optimization and molecular dynamics) software. It can work under linux or windows sistems. Can anybody help me. thanks in advance for any help! cheers, Miguel ******************************************* Miguel Romero, PhD. Fundacisn Hospital Carlos Haya Avda. Carlos Haya 82, Pabellsn A, 7*planta 29010 Malaga Spain Phone: +34 952307928 Fax: +34 951030447 web: http://www.fhch.net e-mail: mromero.-at-.imacyt.org ******************************************* -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY.-at-.ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST.-at-.ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow.-at-.nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Apr 29 04:24:36 2004 Received: from aspirine.u-strasbg.fr (aspirine.u-strasbg.fr [130.79.84.250]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3T9OZkh004275 for ; Thu, 29 Apr 2004 04:24:35 -0500 Received: from hit8.pharma.u-strasbg.fr (hit3.u-strasbg.fr [130.79.85.33]) (authenticated) by aspirine.u-strasbg.fr (8.10.2/8.10.2) with ESMTP id i3T8sxf28177; Thu, 29 Apr 2004 10:54:59 +0200 Message-Id: <6.0.3.0.0.20040429112206.0202ff20|at|aspirine.u-strasbg.fr> X-Sender: rognan|at|aspirine.u-strasbg.fr X-Mailer: QUALCOMM Windows Eudora Version 6.0.3.0 Date: Thu, 29 Apr 2004 11:26:48 +0200 To: Szilveszter Juhos , Tom Halgren , chemistry|at|ccl.net From: Didier Rognan Subject: Re: CCL:Validating docking codes In-Reply-To: <20040429085124.GC543|at|computer.org> References: <20040429085124.GC543|at|computer.org> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net At 10:51 29/04/2004, Szilveszter Juhos wrote: >On Wed, Apr 28, 2004 at 05:56:08PM -0400, Tom Halgren wrote: >[a lot of things to clear the database question concerning Glide] > >Sorry for my mistake and thank you very much for the precise answer (I >even messed up ACD with ACS). > >Indeed it is the "Rognan set" I was writing about as that is the only >set I am aware used by many different groups. I do not want to question >the validation of Glide but want to point the lack of a common, freely >available, drug/lead-like decoy set that would ease the comparison of >different docking software. > >Cheers: >Szilva > > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY|at|ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow|at|nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ Dear colleagues, The dataset you are talking about had been designed 5 years ago using rather rough 'drug-likeness' filters when compared to that used now. It is true that comparing different docking tools with permanently-upgraded datasets is very tricky. Anybody interested in getting an actualised set of 1,000 randomly-chosen drug-like compounds with today drug-likeness filters (e.g. OpenEye rules implemented in FILTER) can contact me. Regards, Didier Didier ----------------------------------------------------------------------------------------------- Dr. Didier ROGNAN Directeur de Recherche CNRS UMR 7081 74, route du Rhin, B.P.24 F-67401 Illkirch direct line: +33 (0)3 90 24 42 35 secretary: +33(0)3 90 24 42 20 fax: +33 (0)3 90 24 43 10 mobile: +33 (0)6 89 56 24 46 email: didier.rognan|at|pharma.u-strasbg.fr From chemistry-request@ccl.net Thu Apr 29 06:35:40 2004 Received: from mail.korea.ac.kr (mail.korea.edu [163.152.6.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3TBZckh009441 for ; Thu, 29 Apr 2004 06:35:39 -0500 Received: from mail (mail.korea.ac.kr [163.152.6.20]) by mail.korea.ac.kr (AIX5.1/8.11.6p2/8.11.0) with ESMTP id i3TBXpb150316 for ; Thu, 29 Apr 2004 20:33:51 +0900 Message-ID: <1262031203.1083238431851.JavaMail.hohjai_y{at}korea.ac.kr> Date: Thu, 29 Apr 2004 20:33:51 +0900 (GMT+09:00) From: Hohjai Lee To: chemistry{at}ccl.net Subject: [Q] Input file of IRCMax Method Mime-Version: 1.0 Content-Type: multipart/mixed; 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