From chemistry-request@server.ccl.net Sat Nov 16 20:53:04 2002 Received: from viper.abbott.com ([130.36.44.77]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAH1r4u29151 for ; Sat, 16 Nov 2002 20:53:04 -0500 Received: from abtmr1.abbott.com (abtmr1.abbott.com [10.254.245.1]) by viper.abbott.com (Switch-2.1.4/Switch-2.1.0) with ESMTP id gAH1s8M05642 for ; Sat, 16 Nov 2002 19:54:08 -0600 (CST) Received: from abtapn561.northamerica.intra.abbott.com (localhost [127.0.0.1]) by abtmr1.abbott.com (Switch-2.0.6/Switch-2.0.6) with ESMTP id gAH1r4j13690 for ; Sat, 16 Nov 2002 19:53:04 -0600 (CST) To: chemistry@ccl.net Cc: james.metz@abbott.com Subject: CCL: Differences between soaking versus co-crystallization for protein-ligand complexes X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000 Message-ID: From: james.metz@abbott.com Date: Sat, 16 Nov 2002 19:52:17 -0600 X-MIMETrack: Serialize by Router on ABTAPN561/ESVR/ABBOTT(Release 5.0.5 |September 22, 2000) at 11/16/2002 07:49:01 PM, Serialize complete at 11/16/2002 07:49:01 PM MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_alternative 000A597486256C74_=" This is a multipart message in MIME format. --=_alternative 000A597486256C74_= Content-Type: text/plain; charset="us-ascii" CCL, Is anyone aware of any publications which describe differences between soaking versus co-crystallization for protein-ligand structures? For example, are there reports of significant differences in the ligand conformation? Has anyone analyzed possible differences in energetics of the bound ligand in a structure obtained from soaking versus co- crystallization? What are the differences in protein conformation in addition to space group and packing? Regards, Jim Metz James T. Metz, Ph.D. Research Investigator Chemist GPRD R46Y AP10-2 Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-6100 U.S.A. Office (847) 936 - 0441 FAX (847) 935 - 0548 james.metz@abbott.com --=_alternative 000A597486256C74_= Content-Type: text/html; charset="us-ascii"
CCL,

        Is anyone aware of any publications which describe differences between soaking versus co-crystallization
for protein-ligand structures?  For example, are there reports of significant differences in the ligand conformation?  Has
anyone analyzed possible differences in energetics of the bound ligand in a structure obtained from soaking versus co-
crystallization?  What are the differences in protein conformation in addition to space group and packing?

        Regards,
        Jim Metz

       

James T. Metz, Ph.D.
Research Investigator Chemist

GPRD R46Y AP10-2
Abbott Laboratories
100 Abbott Park Road
Abbott Park, IL  60064-6100
U.S.A.

Office (847) 936 - 0441
FAX    (847) 935 - 0548

james.metz@abbott.com
 --=_alternative 000A597486256C74_=-- From chemistry-request@server.ccl.net Fri Nov 15 15:35:55 2002 Received: from exchange.neokimia.com ([132.210.158.207]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAFKZsD17113 for ; Fri, 15 Nov 2002 15:35:55 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 content-class: urn:content-classes:message Subject: RE: Need your help MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01C28CE6.6893EF8C" Date: Fri, 15 Nov 2002 15:34:34 -0500 Message-ID: X-MS-Has-Attach: yes X-MS-TNEF-Correlator: Thread-Topic: Need your help Thread-Index: AcKM0VRWaYMpVL24Sn+FnkMa04YQ4AAFDTQQ From: "Axel Mathieu" To: "Pong" , This is a multi-part message in MIME format. ------_=_NextPart_001_01C28CE6.6893EF8C Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable What software did you use to generate your conformers? The reason I ask = this is because in software such as Sybyl and MOE, there are specific = functions in the database viewers to measure these descriptors (Insight = should work like these programs also - I never performed conformational = searches in Inshgt!!). Needless to say, although I have never tried it, = if you import your conformations into a database for these programs, you = should theoretically be able to measure these descriptors quite easily = (so long as the atom numbering is the same for all your molecules in the = database - this is more important than the actual molecule in each = entry!). Working in Sybyl and MOE, they both worked when the = conformational search was performed in each its own program (they = obviously all have the same atom names, numbering and typing). But I = understand you dilemme, I've had the same problem to compare = conformational databases of variations of the same molecule (such as = semi-peptidic molecules where only the side chain is chained). If you do = find something that works no matter the source and/or the atom numbering = (which happens to be the problem), could you please send me the = reference?=20 Axel Mathieu, Ph.D. -----Original Message----- From: Pong [mailto:jaturong.pratuangdejkul@lrb.ap-hop-paris.fr]=20 Sent: 15 novembre, 2002 17:53 To: chemistry@ccl.net Subject: CCL:Need your help Dear memeber of CCL, I'm Mr PONG. I would like to have your advice about the program to = calculate the geometry of chemical structure. I mean, to measure the = distance, aggle and dihedral angle. Yes, there are many programs which = is very easy to do that, I know. But I need the program to measure all = compounds at the same time. This was due to I have thousands conformers = generation by systematic search. All have the same atom type and number, = just only different in conformers. Sure! they must be difference in term = of geometry (distance, angle, and torsional angle). Is there any = program? that I can specify the atom that I want to measure, for = example A-B, A-B-C and A-B-C-D for distance, angle, and torsional angle, = respectively. And use this atom point to be calculate for all conformers = in the same time, not need to select one conformer and calculate for = each one. It's not possible to do if i have many thoudsands conformers. = So, if you have any program capable to to that, could you please to = inform me too. I would like to thank for all your kindness to consider = my problem. Thank you . Pong -=3D This is automatically added to each message by mailing script =3D- = CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To = Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: = jkl@ccl.net ------_=_NextPart_001_01C28CE6.6893EF8C Content-Type: text/x-vcard; name="Axel P. Mathieu.vcf" Content-Transfer-Encoding: base64 Content-Description: Axel P. Mathieu.vcf Content-Disposition: attachment; filename="Axel P. Mathieu.vcf" QkVHSU46VkNBUkQNClZFUlNJT046Mi4xDQpOOk1hdGhpZXU7QXhlbDtQLjtEci4NCkZOOkF4ZWwg UC4gTWF0aGlldQ0KT1JHOk5FT0tJTUlBIElOQy4NClRJVExFOkNvbXB1dGF0aW9uYWwgQ2hlbWlz dA0KVEVMO1dPUks7Vk9JQ0U6KDgxOSkgODIwLTY4NDANClRFTDtXT1JLO0ZBWDooODE5KSA4MjAt Njg0MQ0KQURSO1dPUks7RU5DT0RJTkc9UVVPVEVELVBSSU5UQUJMRTo7O0luc3RpdHV0IGRlIFBo YXJtYWNvbG9naWUgZGUgU2hlcmJyb29rZT0wRD0wQTMwMDEgMTJ0aCBBdmUgTm9ydGg7U2hlcmJy b29rZTtRQztKMUwgMVQzO0M9DQphbmFkYQ0KTEFCRUw7V09SSztFTkNPRElORz1RVU9URUQtUFJJ TlRBQkxFOkluc3RpdHV0IGRlIFBoYXJtYWNvbG9naWU9MEQ9MEEzMDAxIDEydGggQXZlIE5vcnRo PTBEPTBBU2hlcmJyb29rZSwgUUMgSjFMIDE9DQpUMz0wRD0wQUNhbmFkYQ0KVVJMO1dPUks6aHR0 cDovL3d3dy5uZW9raW1pYS5jb20NCkVNQUlMO1BSRUY7RkFYOkF4ZWwuTWF0aGlldUBuZW9raW1p YS5jb20NClJFVjoyMDAyMDQwMlQyMjE0MzZaDQpFTkQ6VkNBUkQNCg== ------_=_NextPart_001_01C28CE6.6893EF8C--