From owner-chemistry@ccl.net Thu Jan 3 05:36:00 2008 From: "Carsten Detering detering::biosolveit.de" To: CCL Subject: CCL: How to fix part of the ligand in docking? Message-Id: <-35972-080103051024-9786-i/kYX1HdDDEHy/gHqWB0Fw]-[server.ccl.net> X-Original-From: "Carsten Detering" Date: Thu, 3 Jan 2008 05:10:18 -0500 Sent to CCL by: "Carsten Detering" [detering ~ biosolveit.de] Hi Xiao, FlexX can dock covalently. You can download an evaluation copy here: http://www.biosolveit.de/license/evaluation.html Hope this helps, Carsten __________________________________________________________________ Dr. Carsten Detering; Appl. Scientist detering[*]biosolveit.de Phone: +49-2241-2525-0 / Fax: -525 www.biosolveit.de BioSolveIT GmbH - An der Ziegelei 75 - 53757 St.Augustin - Germany Geschftsfhrer Dr. Christian Lemmen Amtsgericht Siegburg HRB 6261 Hi all, I'm trying to investigate the interactions between a fatty acid chain (which is attached to holo-ACP) and a protein. We have determined the X-ray structure of the complex of the protein and holo-ACP, but the fatty acid chain cannot be determined by X-ray. So I want to get the final conformation of the fatty acid chain in the binding pocket by docking. And my question is how to fix ACP with its phosphopantetheine chain and let the fatty acid chain move during docking ? Is it feasible, or maybe there are some other better ways? Thanks a lot. From owner-chemistry@ccl.net Thu Jan 3 09:06:00 2008 From: "Inbal Tuvi-Arad inbaltu*openu.ac.il" To: CCL Subject: CCL: Continuous Symmetry Measures Message-Id: <-35973-080103071315-10844-f7WBaqZVmoUfBgrx3V2Zkw[A]server.ccl.net> X-Original-From: "Inbal Tuvi-Arad" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Thu, 3 Jan 2008 14:13:39 +0200 MIME-Version: 1.0 Sent to CCL by: "Inbal Tuvi-Arad" [inbaltu]^[openu.ac.il] Dear CCL Subscribers, I would like to inform you about a new website I have recently developed in collaboration with Prof. David Avnir, the Institute of Chemistry, at the Hebrew University: "CoSyM - Continuous symmetry measures": http://telem.openu.ac.il/symmetry/csm.=20 The Website provides tools for calculating continuous symmetry measures online for any molecule given in pdb format, and uses Jmol for three-dimensional visualization. Answers to questions like:=20 * How far is a given molecule from having rotational symmetry? * By how much is one molecule more chiral than the other? * How much of perfect tetrahedricity is there in a distorted tetrahedron? as well as many other related questions can be answered by these tools.=20 A number, on a scale from zero to 100, describes the distance of a given structure from perfect symmetry; or how much chirality it contains; or to what extent it resembles a polyhedron. The approach to all of these questions is based on the same general principle. That general principle is translated into a computational method for measuring the degree of symmetry point groups, from which several additional specific important measures are derived: * Measuring the degree of the basic symmetry elements * Measuring the degree of polyhedral shape content * Measuring the degree of chirality =20 This website can be used by both researchers, teachers and students, and is part of an undergraduate course for chemistry students at the Open University of Israel. I would be very grateful for any feedback, suggestions or comments regarding the Website. Sincerely, Inbal __________________________________________ Dr. Inbal Tuvi-Arad Department of Natural Sciences The Open University of Israel 108 Ravutski St., POB 808,=20 Raanana, 43107, Israel Tel: 972-9-778-1773=20 Fax: 972-9-778-0661 Email: inbaltu.:.openu.ac.il __________________________________________ From owner-chemistry@ccl.net Thu Jan 3 10:40:00 2008 From: "Michel Petitjean ptitjean^itodys.jussieu.fr" To: CCL Subject: CCL: Continuous Symmetry Measures Message-Id: <-35974-080103103311-5044-ItWG7Zx/wQL/p5x9Oqw60A[-]server.ccl.net> X-Original-From: Michel Petitjean Date: Thu, 3 Jan 2008 16:32:59 +0100 (MET) Sent to CCL by: Michel Petitjean [ptitjean _ itodys.jussieu.fr] To: chemistry##ccl.net Subject: CCL: Re: Continuous Symmetry Measures Dear Inbal, There are very few programs able to compute symmetry/chirality measures: thank you very much for having put yours runnable via your web page. The history of symmetry and chirality measures is summarized in my open access paper in Entropy 2003, 5(3), 271-312 (http://www.mdpi.org/entropy/papers/e5030271.pdf) and my freeware QCM may be downloaded from: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#QCM (computes both the degree of chirality and the degree of direct symmetry). Best regards, Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096) CEA Saclay, bat. 528 91191 Gif-sur-Yvette Cedex Phone: +33(0)1 6908 9681 / Fax: +33(0)1 6908 4007 E-mail: petitjean##itodys.jussieu.fr, michel.petitjean##cea.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html Formerly: ITODYS (CNRS, UMR 7086), 1 rue Guy de la Brosse, 75005 Paris, France. ............................................................................. Sent to CCL by: "Inbal Tuvi-Arad" [inbaltu]^[openu.ac.il] Dear CCL Subscribers, I would like to inform you about a new website I have recently developed in collaboration with Prof. David Avnir, the Institute of Chemistry, at the Hebrew University: "CoSyM - Continuous symmetry measures": http://telem.openu.ac.il/symmetry/csm. The Website provides tools for calculating continuous symmetry measures online for any molecule given in pdb format, and uses Jmol for three-dimensional visualization. Answers to questions like:=20 * How far is a given molecule from having rotational symmetry? * By how much is one molecule more chiral than the other? * How much of perfect tetrahedricity is there in a distorted tetrahedron? as well as many other related questions can be answered by these tools.=20 A number, on a scale from zero to 100, describes the distance of a given structure from perfect symmetry; or how much chirality it contains; or to what extent it resembles a polyhedron. The approach to all of these questions is based on the same general principle. That general principle is translated into a computational method for measuring the degree of symmetry point groups, from which several additional specific important measures are derived: * Measuring the degree of the basic symmetry elements * Measuring the degree of polyhedral shape content * Measuring the degree of chirality This website can be used by both researchers, teachers and students, and is part of an undergraduate course for chemistry students at the Open University of Israel. I would be very grateful for any feedback, suggestions or comments regarding the Website. Sincerely, Inbal __________________________________________ Dr. Inbal Tuvi-Arad Department of Natural Sciences The Open University of Israel 108 Ravutski St., POB 808,=20 Raanana, 43107, Israel Tel: 972-9-778-1773=20 Fax: 972-9-778-0661 Email: inbaltu+/-openu.ac.il __________________________________________ From owner-chemistry@ccl.net Thu Jan 3 14:39:00 2008 From: "Inbal Tuvi-Arad inbaltu * openu.ac.il" To: CCL Subject: CCL: Continuous Symmetry Measures Message-Id: <-35975-080103143711-10015-Q0/ba8ktyANAsLcovOkC6g:+:server.ccl.net> X-Original-From: "Inbal Tuvi-Arad" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Thu, 3 Jan 2008 21:37:40 +0200 MIME-Version: 1.0 Sent to CCL by: "Inbal Tuvi-Arad" [inbaltu()openu.ac.il] Dear Michel, Thank you for your comments. Your paper looks interesting and I'll be happy to read it. Best wishes, Inbal -----Original Message----- > From: owner-chemistry _ ccl.net [mailto:owner-chemistry _ ccl.net]=20 Sent: Thursday, January 03, 2008 5:33 PM To: Inbal Tuvi-Arad Subject: CCL: Continuous Symmetry Measures Sent to CCL by: Michel Petitjean [ptitjean _ itodys.jussieu.fr] To: chemistry~!~ccl.net Subject: CCL: Re: Continuous Symmetry Measures Dear Inbal, There are very few programs able to compute symmetry/chirality measures: thank you very much for having put yours runnable via your web page. The history of symmetry and chirality measures is summarized in my open access paper in Entropy 2003, 5(3), 271-312 (http://www.mdpi.org/entropy/papers/e5030271.pdf) and my freeware QCM may be downloaded from: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#QCM (computes both the degree of chirality and the degree of direct symmetry). Best regards, Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096) CEA Saclay, bat. 528 91191 Gif-sur-Yvette Cedex Phone: +33(0)1 6908 9681 / Fax: +33(0)1 6908 4007 E-mail: petitjean~!~itodys.jussieu.fr, michel.petitjean~!~cea.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html Formerly: ITODYS (CNRS, UMR 7086), 1 rue Guy de la Brosse, 75005 Paris, France. ........................................................................ ..... Sent to CCL by: "Inbal Tuvi-Arad" [inbaltu]^[openu.ac.il] Dear CCL Subscribers, I would like to inform you about a new website I have recently developed in collaboration with Prof. David Avnir, the Institute of Chemistry, at the Hebrew University: "CoSyM - Continuous symmetry measures": http://telem.openu.ac.il/symmetry/csm. The Website provides tools for calculating continuous symmetry measures online for any molecule given in pdb format, and uses Jmol for three-dimensional visualization. Answers to questions like:=3D20 * How far is a given molecule from having rotational symmetry? * By how much is one molecule more chiral than the other? * How much of perfect tetrahedricity is there in a distorted tetrahedron? as well as many other related questions can be answered by these tools.=3D20 A number, on a scale from zero to 100, describes the distance of a given structure from perfect symmetry; or how much chirality it contains; or to what extent it resembles a polyhedron. The approach to all of these questions is based on the same general principle. That general principle is translated into a computational method for measuring the degree of symmetry point groups, from which several additional specific important measures are derived: * Measuring the degree of the basic symmetry elements * Measuring the degree of polyhedral shape content * Measuring the degree of chirality This website can be used by both researchers, teachers and students, and is part of an undergraduate course for chemistry students at the Open University of Israel. I would be very grateful for any feedback, suggestions or comments regarding the Website. Sincerely, Inbal __________________________________________ Dr. Inbal Tuvi-Arad Department of Natural Sciences The Open University of Israel 108 Ravutski St., POB 808,=3D20 Raanana, 43107, Israel Tel: 972-9-778-1773=3D20 Fax: 972-9-778-0661 Email: inbaltu+/-openu.ac.il __________________________________________ -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jan 3 16:21:01 2008 From: "Mikko Huhtala mhuhtala . abo.fi" To: CCL Subject: CCL: Contactos: a program for analysis of docking results Message-Id: <-35976-080103153058-2872-hJ8diRtwDgdyHOokCHE0ow__server.ccl.net> X-Original-From: "Mikko Huhtala" Date: Thu, 3 Jan 2008 15:30:54 -0500 Sent to CCL by: "Mikko Huhtala" [mhuhtala[-]abo.fi] We needed a tool to cluster a set of small-molecule docking results for which RMSD did not work very well as a measure of similarity. I ended up writing a small, 530-line Python program named Contactos. It calculates similarity values based on ligand -- protein contacts, which are independent of the superposition and conformation of the docked solutions. The program can also calculate similarities between different molecules docked to one receptor. Contactos produces a matrix of similarity values, which can be used to cluster the docking results using an external clustering tool, such as MCL by Stijn van Dongen. Contactos itself does not include clustering. Both Contactos and MCL are distributed under the GPL license. Read more and download at http://web.abo.fi/~mhuhtala/contactos.html Mikko Huhtala From owner-chemistry@ccl.net Thu Jan 3 20:49:00 2008 From: "Thomas Joe alabarae\a/yahoo.com" To: CCL Subject: CCL: how to calculate electronic interaction energy Message-Id: <-35977-080103204640-20553-rIOMkiC5z4nv1eQeEmh0GQ ~ server.ccl.net> X-Original-From: "Thomas Joe" Date: Thu, 3 Jan 2008 20:46:35 -0500 Sent to CCL by: "Thomas Joe" [alabarae*_*yahoo.com] I would like to calculate these following parameters 1. Molecular Planarity (area/depth2 ratio) 2. Electronic Interaction Energy (difference between E homo and E Lomo) 3. length/ Width ratio. how to do this. I have referred some papers from CMC. But I don,t have the tools to calcualte those parameters. Your kind help is deeply appreciated. Thomas