From chemistry-request@ccl.net Thu Dec 18 16:33:00 2003 Received: from penguin.dq.fct.unl.pt (penguin.dq.fct.unl.pt [193.136.125.112]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBILWR8a011697 for ; Thu, 18 Dec 2003 16:32:28 -0500 Received: from starquest.dq.fct.unl.pt (srt1.dq.fct.unl.pt [193.136.125.97]) by penguin.dq.fct.unl.pt (Postfix) with ESMTP id 676B43FA3B for ; Thu, 18 Dec 2003 21:32:27 +0000 (WET) Message-Id: <5.2.0.9.0.20031218212515.0239c460[at]pop2.dq.fct.unl.pt> X-Sender: st0015[at]pop2.dq.fct.unl.pt X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Thu, 18 Dec 2003 21:33:38 +0000 To: chemistry[at]ccl.net From: "Antonio M. Nunes" Subject: Chemo-Informatics Statistics Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hBILX08a011816 Dear CCl ers! I'm a chemistry student working on a paper and I needed some statistical info on the evolution of Chemo-informatics. Since article submission is usually a good indicator, does anyone have any idea on where to find this kind of information? Or better yet, does anyone have the information about the amount of papers submited during the years on this subject? :-) Thanks! Antsnio M. Nunes Dep. Qummica - FCT/Univ. Nova de Lisboa, 2829 - 515 Caparica, Portugal PGP: 9841 4219 05DB DEE2 196E 8842 7243 9F1A E991 F190 From chemistry-request@ccl.net Thu Dec 18 15:20:34 2003 Received: from uis-gumail-2.georgetown.edu (postoffice-2.georgetown.edu [141.161.1.110]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBIKK28a030830 for ; Thu, 18 Dec 2003 15:20:02 -0500 Received: from georgetown.edu (mailhost.georgetown.edu [141.161.1.103]) by uis-gumail-2.georgetown.edu (8.12.10/8.12.10) with ESMTP id hBIKK2qr026062 for ; Thu, 18 Dec 2003 15:20:02 -0500 (EST) From: To: chemistry|at|ccl.net Message-ID: Date: Thu, 18 Dec 2003 12:20:02 -0800 X-Mailer: Netscape Webmail MIME-Version: 1.0 Content-Language: en Subject: why Different docking & scoring functions X-Accept-Language: en Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit X-GU-FilterVersion: 1.22 X-Scanned-By: MIMEDefang 2.36 X-Spam-Status: No, hits=1.4 required=7.0 tests=FROM_ENDS_IN_NUMS,NO_REAL_NAME,X_ACCEPT_LANG version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear ALL: NEW YEAR GREETINGS! while thinking off about docking programs: 1. Why do actually we use different docking programs for thier predictions of lead compounds,etc. 2. Why different scoring functions needed. could anybody point out some references/reasons about that About GENERAL: 1. where do i find some good references about computational chemistry & structural informatics. 2. where do i find programs that deals with the solvation especially for drug discovery. Thanks in advance, Sivanesan D.Sivanesan, Ph.D. Dept. of Oncology, Lombardi Cancer Center (NCI Comprehensive Cancer Center), Georgetown University, DC 20057 Phone: 202-687-6338 From chemistry-request@ccl.net Fri Dec 19 04:32:08 2003 Received: from web15404.mail.cnb.yahoo.com (web15404.mail.cnb.yahoo.com [202.43.216.207]) by server.ccl.net (8.12.8/8.12.8) with SMTP id hBJ9VP8a000761 for ; Fri, 19 Dec 2003 04:31:26 -0500 Message-ID: <20031219093124.12312.qmail)at(web15404.mail.cnb.yahoo.com> Received: from [218.244.59.32] by web15404.mail.cnb.yahoo.com via HTTP; Fri, 19 Dec 2003 17:31:24 CST Date: Fri, 19 Dec 2003 17:31:24 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: contour maps in Sybyl To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.1 required=7.0 tests=DATE_IN_PAST_12_24 version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, As you know, the contour maps in Sybyl are always displayed with "Color legend". And my question is focused on the "Color legend". Take the steric contour maps as an example; in general, scattered green areas are regions where bulky substituents are desirable, yellow areas are undesirable. In the "Color legend", green color account for 80% and yellow 20%. I don't know why green should be 80%. And could it be 50% or anything else? Can anyone here give me some explanation on the meaning of "Color legend", and how to control the "Color legend" in a reasonable way? I will appreciate for your any suggestions. Thank you very much in advance. Best regards, Jinsong ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong)at(yahoo.com.cn __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chemistry-request@ccl.net Fri Dec 19 06:03:15 2003 Received: from mail2.nnit.dk (mail2.nnit.dk [152.73.7.112]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBJB2h8a002946 for ; Fri, 19 Dec 2003 06:02:44 -0500 Received: from localhost (localhost.novonordisk.com [127.0.0.1]) by localhost.novonordisk.com (Postfix) with ESMTP id 5C148204114 for ; Fri, 19 Dec 2003 12:02:43 +0100 (CET) Received: from mail2.nnit.dk ([127.0.0.1]) by localhost (mail8k-ext.novo.dk [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 22782-15 for ; Fri, 19 Dec 2003 12:02:42 +0100 (CET) Received: from mail9m-int.novo.dk (mail9m-int.novo.dk [10.1.13.98]) by mail8k-ext.novo.dk (Postfix) with ESMTP id 4CFCF204137 for ; Fri, 19 Dec 2003 12:02:42 +0100 (CET) Received: from EXDKHUB071.corp.novocorp.net (exdkhub071.corp.novocorp.net [10.1.35.71]) by mail9m-int.novo.dk (Postfix) with ESMTP id 48B61148013 for ; Fri, 19 Dec 2003 12:02:42 +0100 (CET) Received: from EXDKHUB040.corp.novocorp.net ([10.1.14.153]) by EXDKHUB071.corp.novocorp.net with Microsoft SMTPSVC(5.0.2195.5329); Fri, 19 Dec 2003 12:02:41 +0100 Received: from exdkba020.corp.novocorp.net ([10.1.26.1]) by EXDKHUB040.corp.novocorp.net with Microsoft SMTPSVC(5.0.2195.5329); Fri, 19 Dec 2003 12:02:41 +0100 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C3C61F.9A055AA3" X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 Subject: CCL: Free software to identify and characterize internal cavities within proteins Date: Fri, 19 Dec 2003 12:02:32 +0100 Message-ID: <76F96CFE2AA2114C886B028A065A7FC4DD7F1D)at(exdkba020.novo.dk> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL: Free software to identify and characterize internal cavities within proteins Thread-Index: AcPGGRtGDD6f58AiQRS3+IbZdMuj1AABmxxA From: "LEDM (Leonardo De Maria)" To: X-OriginalArrivalTime: 19 Dec 2003 11:02:41.0090 (UTC) FILETIME=[9F081A20:01C3C61F] X-Virus-Scanned: by amavisd-new/catpipe/nnit at nnit.dk X-Spam-Status: No, hits=2.5 required=7.0 tests=FORGED_RCVD_TRAIL,HTML_40_50,HTML_MESSAGE version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------_=_NextPart_001_01C3C61F.9A055AA3 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable > Hi everyone, >=20 > we are interested in a free software to identify and characterize = internal cavities within proteins. >=20 > The information we would like to have is: size of the cavity (volume = and surface) and protein atoms belonging > to it.=20 >=20 > Any help from out there? I'll summarize the answers. >=20 > Thanks is advance and happy holidays, >=20 > Leonardo De Maria, Ph.D. > Research Scientist > Novozymes A/S > Sm=F8rmosevej 25 > 2880 Bagsv=E6rd > Denmark >=20 > Phone: +45 44421890 > Fax: +45 44980246 >=20 > e.mail: ledm)at(novozymes.com >=20 >=20 ------_=_NextPart_001_01C3C61F.9A055AA3 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable CCL: Free software to identify and characterize internal = cavities within proteins

Hi everyone,

we are interested in a free software to = identify and characterize internal cavities within proteins.

The information we would like to have = is: size of the cavity (volume and surface) and protein atoms = belonging
to it.

Any help from out there? I'll summarize = the answers.

Thanks is advance and happy = holidays,

Leonardo De Maria, Ph.D.
Research Scientist
Novozymes A/S
Sm=F8rmosevej 25
2880 Bagsv=E6rd
Denmark

Phone:  +45 44421890
Fax:      = +45 44980246

e.mail: = ledm)at(novozymes.com


------_=_NextPart_001_01C3C61F.9A055AA3-- From chemistry-request@ccl.net Fri Dec 19 11:41:42 2003 Received: from fulcrum.physbio.mssm.edu (fulcrum.physbio.mssm.edu [146.203.4.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBJGfB8a001396 for ; Fri, 19 Dec 2003 11:41:11 -0500 Received: from mceruso (helo=localhost) by fulcrum.physbio.mssm.edu with local-esmtp (Exim 4.14) id 1AXNgc-001RuD-6e; Fri, 19 Dec 2003 11:41:10 -0500 Date: Fri, 19 Dec 2003 11:41:10 -0500 From: Marc Ceruso To: "LEDM (Leonardo De Maria)" cc: CHEMISTRY|at|ccl.net Subject: Re: CCL:Free software to identify and characterize internal cavities within proteins In-Reply-To: <76F96CFE2AA2114C886B028A065A7FC4DD7F1D|at|exdkba020.novo.dk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN X-Spam-Status: No, hits=-1.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id hBJGfg8a001457 Hello- I think SURFNET by Roman Laskowski may work for you http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html Cheers Marc ________________________________________________________________________________ Department of Physiology & Biophysics Mt Sinai School of Medicine One Gustave L. Levy Place New York NY 10029 Tel : 212-241 82 93 Fax : 212-860 33 69 mceruso|at|physbio.mssm.edu ________________________________________________________________________________ On Fri, 19 Dec 2003, LEDM (Leonardo De Maria) wrote: > > Hi everyone, > > > > we are interested in a free software to identify and characterize internal cavities within proteins. > > > > The information we would like to have is: size of the cavity (volume and surface) and protein atoms belonging > > to it. > > > > Any help from out there? I'll summarize the answers. > > > > Thanks is advance and happy holidays, > > > > Leonardo De Maria, Ph.D. > > Research Scientist > > Novozymes A/S > > Smxrmosevej 25 > > 2880 Bagsvfrd > > Denmark > > > > Phone: +45 44421890 > > Fax: +45 44980246 > > > > e.mail: ledm|at|novozymes.com > > > > >