From owner-chemistry@ccl.net Fri Oct 12 03:30:00 2007 From: "Bala subramanian bala%x%igib.res.in" To: CCL Subject: CCL: question on complex stability Message-Id: <-35371-071012032741-4651-D//JgZq5G0xhfsI+mRnPQw,,server.ccl.net> X-Original-From: "Bala subramanian" Date: Fri, 12 Oct 2007 03:27:38 -0400 Sent to CCL by: "Bala subramanian" [bala*|*igib.res.in] Dear users, I carried MD simulation of two complexes say A and B, in explicit water (same ligand with two different receptor) and did MMPBSA analysis (for the snapshots obtained from complex trajectories). The absolute energy of the complex A obtained from MMPBSA is less than that of complex B, but the free energy of binding shows a reverse trend. In such cases, how one can choose the best complex. I would appreciate if anybody could provide me some suggestion on the same. Thanks in advance, Bala From owner-chemistry@ccl.net Fri Oct 12 10:55:01 2007 From: "yoana perez badel yoa^fq.uh.cu" To: CCL Subject: CCL:G: SCF confused Message-Id: <-35372-071012085449-13478-72eM4X6LDugVaKI+PJ4vIg]-[server.ccl.net> X-Original-From: yoana perez badel Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 12 Oct 2007 08:13:49 -0400 (CDT) MIME-Version: 1.0 Sent to CCL by: yoana perez badel [yoa[a]fq.uh.cu] I am using the Counterpoise procedure to correct both the optimized geometry and the interaction energy with Gaussian03 and the following error appears: The SCF is confused. How can I solve this problem? Thanks in advance, Yoana. From owner-chemistry@ccl.net Fri Oct 12 14:19:00 2007 From: "aps1968**googlemail.com" To: CCL Subject: CCL: (re-)relaxing molecules Message-Id: <-35373-071012113112-6039-EsrbTOuQoObhzitdoXSUTg-$-server.ccl.net> X-Original-From: aps1968 _ googlemail.com Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 12 Oct 2007 17:01:48 +0200 MIME-Version: 1.0 Sent to CCL by: aps1968*|*googlemail.com Dear CClrs, in order to perform CoMFA computations in Sybyl, I aligned my already externally optimized molecules with the use of the function MATCH, taking into account the fragment common for all molecules. The referee of the paper however asks if the molecules were re-relaxed after the MATCH procedure. I am not quite sure I understand what he means. Should I again in the new positions perform any further optimization? They are already optimized. He also suggests a pharmacofore based alignment prior to comfa and again asks to consider relaxing the conformers after MATCH alignment prior to comfa. Any comments to that? Which alternative alignment methods can be recommended to a SYBYL user? Regards, Andy From owner-chemistry@ccl.net Fri Oct 12 16:30:01 2007 From: "Mesa Analytics & Computing, LLC mesaac-x-comcast.net" To: CCL Subject: CCL: computer aided drug design course Message-Id: <-35374-071012162457-24655-DfGmdcsIzmVEJPGdxcv0kA..server.ccl.net> X-Original-From: "Mesa Analytics & Computing, LLC" Content-Type: multipart/alternative; boundary="------------090201040805060109000106" Date: Fri, 12 Oct 2007 13:53:20 -0600 MIME-Version: 1.0 Sent to CCL by: "Mesa Analytics & Computing, LLC" [mesaac*_*comcast.net] This is a multi-part message in MIME format. --------------090201040805060109000106 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Omar, You may find the on-line learning modules of the Cheminformatics Virtual Classroom (www.chemvc.com) useful for your course. There's movie demos of each module on the site if you want to get a sense of the utility for pharmacy students. Professors can request accounts for students to use the modules during the course period. The Drug Design module has been connected to the BIOPS site from New Mexico State University Bioinformatics CREST Center. You can view the BIOPS site directly by selecting the Bioinformatics link off of the www.chemvc.com page. Norah -------------------------------------------- Norah MacCuish, Ph.D. CSO Mesa Analytics & Computing, LLC (505)983-3449 phone (509)472-8131 fax www.mesaac.com omar Deeb deeb2000il[A]yahoo.com wrote: > Dear ccl users, > I would like to give a "computer aided drug design" course for the 5th > year pharmacy students. > Any suggestions concerning the course, materials, software, lectures > notes, ppt and others. > Thanks in advance > > Dr. Omar Deeb > Al-Quds University > Jerusalem > > ------------------------------------------------------------------------ > Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user > panel > > and lay it on us. --------------090201040805060109000106 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Omar,

  You may find the on-line learning modules of  the Cheminformatics Virtual Classroom (www.chemvc.com) useful for your course.
There's movie demos of each module on the site if you want to get a sense of the utility for pharmacy students.  Professors can request accounts for students to use the modules during the course period.  The Drug Design module has been connected to the BIOPS site from New Mexico State University  Bioinformatics CREST Center.  You can view the BIOPS site directly by selecting the Bioinformatics link off of the www.chemvc.com page.

Norah
--------------------------------------------
Norah MacCuish, Ph.D.
CSO
Mesa Analytics & Computing, LLC
(505)983-3449 phone
(509)472-8131 fax
www.mesaac.com

omar Deeb deeb2000il[A]yahoo.com wrote:
Dear ccl users,
I would like to give a "computer aided drug design" course for the 5th year pharmacy students.
Any suggestions concerning the course, materials, software, lectures notes, ppt and others.
Thanks in advance
 
Dr. Omar Deeb
Al-Quds University
Jerusalem 

Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user panel and lay it on us.
--------------090201040805060109000106-- From owner-chemistry@ccl.net Fri Oct 12 18:08:00 2007 From: "Dr David N Haney haney^_^edusoft-lc.com" To: CCL Subject: CCL: Protein-Protein scoring/PDB..ligand database Message-Id: <-35375-071012180208-2422-o2DZuQcbvSpEAgwV5k6flQ%a%server.ccl.net> X-Original-From: Dr David N Haney Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Fri, 12 Oct 2007 17:01:16 -0400 Mime-Version: 1.0 Sent to CCL by: Dr David N Haney [haney*_*edusoft-lc.com] Dear CCL: In response to a couple of recent CCL posts: PDB structures and associated ligand database (from Rajarshi Guha) and Protein-Protein scoring - non standard residue (from Gemma Kinsella) I would like to point out the utility of EduSoft's HINT software. HINT is a software that utilizes an empirical force field based on LogP octanol-water data. HINT has been successfully used to calculate protein-protein scoring as well as protein-ligand scoring. This scoring method has been shown to have close association with the experimental binding values for several systems. A comparison of native scoring with HINT scoring for several docking programs has been reported. Although HINT does not currently have unusual amino acids as part of its "dictionary", they can be added to the ASCII table that is used to calulate hydropathy, or the "unusual" components can be calculated with the "calculate" function of HINT. If you have any question please contact me or Prof. Glen Kellogg at VCU. Please see the following references: 1. F.Spyrakis, et al, Eur J Med Chem, 42:(2007)921-933 19 protein-ligand complexes docked with AutoDock, GOLD and FlexX, comparing native and HINT scoring. 2. A.Amadasi, et al, J Mol Biol 358:(2006)289-309 Energetics of Water–Protein and Water–Ligand Interactions for 12 proteins, and 15 protein-ligand complexes 3. M.Fornabaio, et al, J Med Chem 47:(2004)4507-4516 Contribution of Structural Water Molecules in predicted free energy of binding for HIV-1 Protease Complexes 4. M.Fornabaio, et al, J Med Chem 46:(2003)4487-4500 predicted free energy of binding and ionization state, Computational Titration of Neuraminidase-Inhibitor Complexes 5. P.Cozzini, et al, J Med Chem 45:(2002)2469-2483 simple calculations of free energy of binding for protein-ligand complexes (53 examples) 6. J.C.Burnett, et al, Proteins:Struct Funct Genet 42:(2001)355-377 computational method for calculating protein-protein interaction energies using mutant hemoglogin examples, comparison to experimental. http://www.edusoft-lc.com/hint/ -- ######### David N. Haney, Ph.D. ######### # EduSoft, LC Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney%a%edusoft-lc.com # ################# ##################### From owner-chemistry@ccl.net Fri Oct 12 20:00:00 2007 From: "Cesar Millan pachequin:-:gmail.com" To: CCL Subject: CCL: AminoAcid Rotamer Analysis Message-Id: <-35376-071012195740-12085-BbgGIWqRr2KLrAsDdmnSfQ .. server.ccl.net> X-Original-From: "Cesar Millan" Date: Fri, 12 Oct 2007 19:57:35 -0400 Sent to CCL by: "Cesar Millan" [pachequin^^^gmail.com] Hi everyone! I have a couple of protein dynamics made by CHARMM (dcd format) and I want to do a dihedral analysis of the aminoacids on my protein. I knew a program called Dials and Windows that could this kind of analysis, but it only runs on SGI machines. Does anyone knows any free software that could realize this kind of analysis on linux machines? Any help would be appreciate. Best Regards. Cesar.