Call for paper for the Spring 2008 ACS symposium on "Molecular = Modeling Applied on DPP-4 Inhibitor Programs"

From owner-chemistry@ccl.net Wed Sep 19 02:03:01 2007 From: "Szabolcs Csepregi scsepregi[a]chemaxon.com" To: CCL Subject: CCL: Smiles -> Isis draw Message-Id: <-35205-070919020100-4039-YlFieNXJrc2T5kex/YFVSw()server.ccl.net> X-Original-From: Szabolcs Csepregi Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 19 Sep 2007 08:00:52 +0200 MIME-Version: 1.0 Sent to CCL by: Szabolcs Csepregi [scsepregi^^chemaxon.com] Hi Jerome, For smiles -> 2D or 3D molfile conversion you may also use molconvert > from the Marvinbeans package: http://www.chemaxon.com/marvin/doc/user/molconvert.html The applications of Marvinbeans: Molconvert and MarvinSketch/View/Space are free for everyone if used on the desktop without integrating into another application. HTH Szabolcs Szabolcs Csepregi, PhD Director of Search Technologies, ChemAxon Ltd. http://www.chemaxon.com Skype: szabolcs.csepregi Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659 Jerome Kieffer jerome.Kieffer . terre-adelie.org wrote: > Sent to CCL by: Jerome Kieffer [jerome.Kieffer^terre-adelie.org] > Dear CCLers, > > I am wondering if any of yours has a piece of software to convert a > molecule represented as it's SMILES string into a ".skc" isis draw > file. The best would be an open-source code so that I could re-use it > but if it is «just» free, it is OK for me. > > Best regards. > From owner-chemistry@ccl.net Wed Sep 19 03:31:01 2007 From: "immanuel feng feng.immanuel[*]gmail.com" To: CCL Subject: CCL:G: asking for keyword for DFT Message-Id: <-35206-070919032846-20615-FWMCCfQjw99NiXxqmOuQ6g^^^server.ccl.net> X-Original-From: "immanuel feng" Content-Type: multipart/alternative; boundary="----=_Part_9536_30458665.1190186914941" Date: Wed, 19 Sep 2007 15:28:34 +0800 MIME-Version: 1.0 Sent to CCL by: "immanuel feng" [feng.immanuel**gmail.com] ------=_Part_9536_30458665.1190186914941 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all: I am looking for the keyword in Gaussian running DFT methods: HCTHh, BB1K, TPSSh, TPSS. Any answer and suggestion is of great help! Thanks ------=_Part_9536_30458665.1190186914941 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

Dear all:

I am looking for the keyword in Gaussian running DFT methods: HCTHh, BB1K, TPSSh, TPSS. Any answer and suggestion is of great help! Thanks

------=_Part_9536_30458665.1190186914941-- From owner-chemistry@ccl.net Wed Sep 19 04:06:01 2007 From: "Dr. Ponnadurai Ramasami ramchemi~!~intnet.mu" To: CCL Subject: CCL: Problem with symmetry in frequency calculation Message-Id: <-35207-070919034322-25871-ZmIAm2nEq7qRB51By5/qSA]*[server.ccl.net> X-Original-From: "Dr. Ponnadurai Ramasami" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0018_01C7FAB2.BEEC7A40" Date: Wed, 19 Sep 2007 11:46:41 +0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi() intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_0018_01C7FAB2.BEEC7A40 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All We have done optimisation and frequency calculations for the C10O = molecule (long chain carbon). The calculations are completed but with (?) interogation sign in the = symmetry for each frequency calculated. Can anyone advise about this problem? Thanks Ramasami ------=_NextPart_000_0018_01C7FAB2.BEEC7A40 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear All

We have done optimisation and frequency = calculations for the C10O molecule (long chain carbon).

The calculations are completed but with = (?)=20 interogation sign in the symmetry for each frequency = calculated.

Can anyone advise about this = problem?

Thanks

Ramasami

------=_NextPart_000_0018_01C7FAB2.BEEC7A40-- From owner-chemistry@ccl.net Wed Sep 19 04:44:01 2007 From: "Arvydas Tamulis tamulis**mserv.itpa.lt" To: CCL Subject: CCL: Cartesian coordinates of Retinal molecule Message-Id: <-35208-070919034440-26742-2aeQb10ZPiTJxXKXmUXz1g%a%server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 19 Sep 2007 09:53:15 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis],[mserv.itpa.lt] Dear Colleagues, Would you please to send me the Cartesian coordinates of Retinal molecule. Better if you will send me few sets of coordinates: 1) all-trans, 2) 9-cis, 11-cis, 13-cis optimized in ground and excited states by DFT method or will say references who already published these results. Thanking your in advance. With best regards, Arvydas Tamulis From owner-chemistry@ccl.net Wed Sep 19 07:39:00 2007 From: "Daniel Jana dfjana_._gmail.com" To: CCL Subject: CCL:G: asking for keyword for DFT Message-Id: <-35209-070919072930-7981-ZCu3eBnH8A98O2NDtLFodA*_*server.ccl.net> X-Original-From: "Daniel Jana" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 19 Sep 2007 12:22:59 +0100 MIME-Version: 1.0 Sent to CCL by: "Daniel Jana" [dfjana++gmail.com] On 19/09/2007, immanuel feng feng.immanuel[*]gmail.com wrote: > Dear all: > I am looking for the keyword in Gaussian running DFT methods: HCTHh, > BB1K, TPSSh, TPSS. Any answer and suggestion is of great help! Thanks Hello http://comp.chem.umn.edu/info/DFT.htm This page sums up some recent methods and explains how to use them. Unfortunately, from the ones you asked, it only has the keyword for BB1K. Hope it helps, Daniel Jana From owner-chemistry@ccl.net Wed Sep 19 09:54:00 2007 From: "Gao, Ying-Duo yingduo_gao%%merck.com" To: CCL Subject: CCL: Call for paper for the Spring 2008 ACS symposium on "Molecular Modeling Applied on DPP-4 Inhibitor Programs" Message-Id: <-35210-070919094256-6998-OrvLLQS/lI8RGDw/I2r21w-,-server.ccl.net> X-Original-From: "Gao, Ying-Duo" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7FABC.8B018D8F" Date: Wed, 19 Sep 2007 08:56:49 -0400 MIME-Version: 1.0 Sent to CCL by: "Gao, Ying-Duo" [yingduo_gao%%merck.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C7FABC.8B018D8F Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable > Dear Colleagues, > =20 > You are invited to submit papers for the symposium on "Molecular > Modeling Applied on DPP-4 Inhibitor Programs." This symposium will > take place as part of the COMP section at the 235th American Chemical > Society National Meeting, April 6-10, 2008, in New Orleans.=20 > =20 > Dipeptidyl peptidase IV (DPP-4) inhibitor is a new promising approach > for treating type 2 diabetes. Many pharmaceutical/biotech companies > have had a drug discovery program on DPP-4 inhibitors where molecular > modeling, such as virtual screening, structure-based drug design, > QSAR, have been used extensively for accelerating the discovery > process. The idea of this symposium is to bring scientists together > from both pharmaceutical/biotech industry and academic to discuss > modeling approaches and share experiences on the DPP-4 inhibitor > programs. =20 > =20 > This symposium may include but not limited to topics like:=20 >=20 > 1. Virtual screening for lead identification;=20 > 2. Structure-based design;=20 > 3. QSAR approaches for improving potency, selectivity;=20 > 4. Homology modeling of DPP-4 and related enzymes, such as DPP-8, > DPP-9, FAP;=20 > 5. Attenuating off-target activities and solving ADMET issues. =20 >=20 > All are invited to participate and submit abstracts for this session. > Please use the OASYS to submit your abstract. You can access the COMP > symposia at OASYS via > =20 > http://oasys.acs.org/acs/235nm/comp/papers/index.cgi=20 >=20 > Select "Oral: Molecular Modeling Applied on DPP-4 Inhibitor Programs" > as Topic, then follow the instruction on the page.=20 >=20 > The deadline for submitting abstract is October 28, 2007. >=20 > Best regards, >=20 > Symposium organizer >=20 > Ying-Duo Gao (Ph. D.)=20 > Molecular Systems=20 > Merck Research Labs.=20 > P.O. Box 2000, RY50-SW100=20 > Rahway, NJ 07065=20 >=20 > 732-594-6024 (tel)=20 > 732-594-4224 (fax)=20 > yingduo_gao.:.merck.com=20 >=20 ---------------------------------------------------------------------------= --- Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is=20 available at http://www.merck.com/contact/contacts.html) that may be=20 confidential, proprietary copyrighted and/or legally privileged. It is=20 intended solely for the use of the individual or entity named on this=20 message. If you are not the intended recipient, and have received this=20 message in error, please notify us immediately by reply e-mail and then=20 delete it from your system. ---------------------------------------------------------------------------= --- ------_=_NextPart_001_01C7FABC.8B018D8F Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: quoted-printable Call for paper for the Spring 2008 ACS symposium on "Molecular = Modeling Applied on DPP-4 Inhibitor Programs"

Dear = Colleagues,

You are invited to = submit papers for the symposium on "Molecular Modeling Applied on DPP-= 4= Inhibitor Programs." This symposium will take place as part of the = COMP section at the 235th American Chemical Society National Meeting, April= = 6-10, 2008, in New Orleans.

Dipeptidyl peptidase= = IV (DPP-4) inhibitor is a new promising approach for treating type 2 = diabetes. Many pharmaceutical/biotech companies = have had a drug discovery program on DPP-4 inhibitors where molecular = modeling, such as virtual screening, structure-based drug design, QSAR, hav= e= been used extensively for accelerating the discovery process. The idea of = this symposium is to bring scientists together from both = pharmaceutical/biotech industry and academic to discuss modeling = approaches and share experiences on the DPP-4 inhibitor = programs.

This symposium may = include but not limited to topics like:

1. Virtual screening = =66or lead identification;
2. Structure-based = design;
3. QSAR approaches = =66or improving potency, selectivity;
4. Homology modeling= = of DPP-4 and related enzymes, such as DPP-8, DPP-9, FAP;
5. Attenuating = off-target activities and solving ADMET issues.

All are invited to = participate and submit abstracts for this session. Please use the OASYS= = to submit your abstract. You can access the COMP symposia at OASYS = via

http://oasys.acs.org/acs/235nm/comp/papers/index.cgi

Select "Oral: = Molecular Modeling Applied on DPP-4 Inhibitor Programs" as Topic, then= = =66ollow the instruction on the page.

The deadline for = submitting abstract is October 28, 2007.

Best = regards,

Symposium = organizer

Ying-Duo Gao (Ph. D.)= =
Molecular Systems =
Merck Research Labs.= =
P.O. Box 2000, = RY50-SW100
Rahway, NJ 07065 =

732-594-6024 (tel) =
732-594-4224 (fax) =
yingduo_gao.:.merck.co= m=

----------------------------------------------------------------------=
--------
Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD
and in Japan, as Banyu - direct contact information for affiliates is=20
available at http://www.merck.com/contact/contacts.html) that may be=20
confidential, proprietary copyrighted and/or legally privileged. It is=20
intended solely for the use of the individual or entity named on this=20
message. If you are not the intended recipient, and have received this=20
message in error, please notify us immediately by reply e-mail and then=20
delete it from your system.

---------------------------------------------------------------------------=
---

------_=_NextPart_001_01C7FABC.8B018D8F-- From owner-chemistry@ccl.net Wed Sep 19 13:54:01 2007 From: "Curt M. Breneman brenec\a/rpi.edu" To: CCL Subject: CCL: Model Domain Applicability Symposium at ACS National Meeting in New Orleans - 2008 Message-Id: <-35211-070919115325-8416-Gf932Oxxv/lQaTgr9uK80A!=!server.ccl.net> X-Original-From: "Curt M. Breneman" Content-Type: multipart/alternative; boundary="----=_NextPart_000_00F8_01C7FAA9.F53D70D0" Date: Wed, 19 Sep 2007 10:43:46 -0400 MIME-Version: 1.0 Sent to CCL by: "Curt M. Breneman" [brenec.[-].rpi.edu] This is a multi-part message in MIME format. ------=_NextPart_000_00F8_01C7FAA9.F53D70D0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit FIRST Announcement: Model Domain Applicability Symposium - ACS New Orleans 2008 "Model Applicability Domains: When should I use my model?" Organizers: Curt Breneman and Dan Ortwine It is often the case that a predictive modeling method will be misapplied by new practictioners, resulting in the loss of local credibility in an otherwise valuable technique. This problem is exacerbated by the availability of sophisticated tools with numerous tuning parameters. Even the use of default values can often result in less than optimal performance. Clearly, this problem is widespread and deserves attention. This issue extends well beyond QSAR and QSPR prospective modeling exercises, and includes docking, scoring, ADME/Tox predictions and many other situations where empirical or semi-empirical techniques are utilized to classify, rank-order or predict chemical behavior. Please consider contributing a talk to this important symposium, so we can expose the state of the art in "best practices" for model application, and move the field of prospective modeling forward. See you in New Orleans! Cheers, Curt Breneman RPI Chemistry Director, RECCR Center ------=_NextPart_000_00F8_01C7FAA9.F53D70D0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

FIRST Announcement: Model Domain Applicability Symposium – ACS New = Orleans 2008

“Model Applicability = Domains: When should I use my model?”

Organizers: Curt Breneman = and Dan Ortwine

It is often the case that a predictive modeling method will be misapplied by new practictioners, resulting in the loss of local = credibility in an otherwise valuable technique. This problem is exacerbated by = the availability of sophisticated tools with numerous tuning = parameters. Even the use of default values can often result in less than optimal performance. = Clearly, this problem is widespread and deserves = attention.

This issue extends well beyond QSAR and QSPR prospective = modeling exercises, and includes docking, scoring, ADME/Tox predictions and many = other situations where empirical or semi-empirical techniques are utilized to classify, rank-order or predict chemical behavior. =

Please consider contributing a talk to this important symposium, = so we can expose the state of the art in “best practices” for = model application, and move the field of prospective modeling = forward.

See you in New = Orleans!

Cheers,

Curt Breneman

RPI Chemistry

Director, RECCR Center

------=_NextPart_000_00F8_01C7FAA9.F53D70D0-- From owner-chemistry@ccl.net Wed Sep 19 14:55:01 2007 From: "Agrinaldo Jacinto do Nasimento jr. agrinaldo18 _ yahoo.com.br" To: CCL Subject: CCL: Vertical Ionization Energy Message-Id: <-35212-070919112729-6550-5cY3l86rit5A2Rgsg74OWQ.:.server.ccl.net> X-Original-From: "Agrinaldo Jacinto do Nasimento jr." Date: Wed, 19 Sep 2007 11:27:26 -0400 Sent to CCL by: "Agrinaldo Jacinto do Nasimento jr." [agrinaldo18::yahoo.com.br] Hi... Anyone knows some experimental database with vertical Ionization Energy values ?? Thank you in advance for your help. Agrinaldo J. do Nascimento Jr. Universidade Federal de Pernambuco agrinaldo18++yahoo.com.br From owner-chemistry@ccl.net Wed Sep 19 17:12:01 2007 From: "David Hose anthrax_brothers+*+hotmail.com" To: CCL Subject: CCL: Vertical Ionization Energy Message-Id: <-35213-070919171049-28091-BSDSlnEqxCT3EIxdhbCpRw=server.ccl.net> X-Original-From: "David Hose" Date: Wed, 19 Sep 2007 17:10:45 -0400 Sent to CCL by: "David Hose" [anthrax_brothers..hotmail.com] Agrinaldo, The NIST Chemistry Webbook has Ionisation energies: http://webbook.nist.gov/chemistry/ As does the Computational Chemistry Comparison and Benchmark DataBase (CCCBDB): http://srdata.nist.gov/cccbdb/ Regards, Dave. Hi... Anyone knows some experimental database with vertical Ionization Energy values ?? Thank you in advance for your help. Agrinaldo J. do Nascimento Jr. Universidade Federal de Pernambuco agrinaldo18-*-yahoo.com.br From owner-chemistry@ccl.net Wed Sep 19 22:12:01 2007 From: "Sean Ekins ekinssean++yahoo.com" To: CCL Subject: CCL: New Computational Toxicology Book Message-Id: <-35214-070919175744-17978-2Z2evf40bvRHciCvbCNepA%server.ccl.net> X-Original-From: "Sean Ekins" Date: Wed, 19 Sep 2007 17:57:40 -0400 Sent to CCL by: "Sean Ekins" [ekinssean^^^yahoo.com] Just wanted to bring the following books to your attention which I was involved in editing and soliciting contributions from some well known groups "Computational Toxicology: Risk Assessment for Pharmaceutical and Environmental Chemicals" and "Computer Applications in Pharmaceutical Research and Development" published by Wiley. http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470049626,descCd-tableOfContents.html http://www.wiley.com/WileyCDA/WileyTitle/productCd-0471737798.html I would also be happy if there was any feedback from readers etc. Sincerely Sean Ekins ekinssean#,#yahoo.com