From owner-chemistry@ccl.net Thu Mar 13 05:51:00 2008 From: "Modelling & Design of Molecular Materials mdmm*|*mml.ch.pwr.wroc.pl" To: CCL Subject: CCL: MDMM 2008 - early bird deadline Message-Id: <-36495-080313053802-3615-DhwmOOWA/ZR45mIP1buIUQ-$-server.ccl.net> X-Original-From: Modelling & Design of Molecular Materials Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 13 Mar 2008 09:44:27 +0100 MIME-Version: 1.0 Sent to CCL by: Modelling & Design of Molecular Materials [mdmm-*-mml.ch.pwr.wroc.pl] Dear colleagues, The deadline for early bird registration for Modelling and Design of Molecular Materials 2008 is almost up. Registration and more information about the conference, which will take place in Piechowice, Poland, June 23-28, 2008, is available at the conference web page: http://mml.ch.pwr.wroc.pl/mdmm2008 Modelling and Design of Molecular Materials is a biannual conference devoted to presenting contemporary computational methods along with their applications in molecular modelling and molecular material design and related fields. Planned sessions include: * catalyst design * drug design * design of materials for electronics * new computational methods * structural genomics * biopolymer structure prediction * modelling chemical reactions * modeling intermolecular interactions Refereed conference proceedings will be published in the Journal of Molecular Modeling. Proceedings from previous conferences can be found in the same journal - in the July 2007 issue from MDMM 2006 and in the September 2005 issue from MDMM 2004. Some contributions from the 2004 meeting have also appeared in the Springer book volume Molecular Materials with Specific Interactions: Modeling & Design. Hope to see you in Piechowice, MDMM 2008 organizers -- Modelling and Design of Molecular Materials 2008 June 23-28 - Piechowice, Poland Conference webpage: http://www.mml.ch.pwr.wroc.pl/mdmm2008 From owner-chemistry@ccl.net Thu Mar 13 09:57:00 2008 From: "Julien Lefeuvre j.lefeuvre- -iecb.u-bordeaux.fr" To: CCL Subject: CCL: Characterization of binding pocket (hydrophobic or hydrophilic) ? Message-Id: <-36496-080313091731-642-cQh0tjDwxnUX350HDx7A/w^^server.ccl.net> X-Original-From: Julien Lefeuvre Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 13 Mar 2008 13:46:05 +0100 MIME-Version: 1.0 Sent to CCL by: Julien Lefeuvre [j.lefeuvre\a/iecb.u-bordeaux.fr] Tiejun Cheng tjcheng^-^mail.sioc.ac.cn wrote: > Sent to CCL by: "Tiejun Cheng" [tjcheng::mail.sioc.ac.cn] > Dear CCLers, > > Is there any methods or softwares that can determine whether a binding pocket is hydrophobic or hydrophilic? Thanks in advance. > > Best regards, > > Jay Hi Jay, I am not sure if it will fit your needs, but I wrote "pymlp" to calculate lipophilicity potential maps of protein for vmd and pymol. Pymlp is a refurbished version of some former fortran code called MLPP. You may found it here: http://code.google.com/p/pymlp/ The code is a bit slow right now and I have some much faster code in house ... but it needs more time before release. ============================= pyMLP: Molecular Lipophilicity Potential evaluator pyMLP is a program computing the molecular lipophilicity potential map of proteins. -------------------------------------------------------------------------------- Please include this reference in published work using pyMLP: Broto P., Moreau G., Vandycke C. - `Molecular structures: Perception, autocorrelation descriptor and sar studies. System of atomic contributions for the calculation of the n-octanol/water partition coefficients', Eu. J. Med. Chem. 1984, 19.1, 71-78 Laguerre M., Saux M., Dubost J.P., Carpy A. - `MLPP: A program for the calculation of molecular lipophilicity potential in proteins', Pharm. Sci. 1997, 3.5-6, 217-222 -------------------------------------------------------------------------------- This program was developed in python as a platform independent equivalent of MLPP (see references). As a result pyMLP may run on any platform supported by Python and Numpy. ============================= HIH Julien Lefeuvre From owner-chemistry@ccl.net Thu Mar 13 10:31:00 2008 From: "Barry Hardy barry.hardy||vtxmail.ch" To: CCL Subject: CCL: eCheminfo Hands-on Drug Discovery Workshop in Oxford Message-Id: <-36497-080313095910-9259-KUvnffpA4+78ZdwjpQR9TQ^^server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 13 Mar 2008 13:58:48 +0100 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy+/-vtxmail.ch] The 5 Day eCheminfo Hands-on Drug Discovery Workshop Week will take place this year 21-25 July 2008 at the Medical Sciences Teaching Center, Oxford University, Oxford, UK. Topics to be covered include Virtual Screening & Docking; Structure-based Drug Design; Ligand Optimisation & Library Design; Structure Search, Similarity and Property Estimation; Data Mining, Analysis & Visualisation; Pharmacophore Modelling for Lead Identification; Fragment-based Drug Design; QSAR-based Predictive Toxicology; and Quantitative Spectrometric Data-Activity Relationship Modelling. These workshops are aimed to provide a set of stimulating workshops using latest advanced modelling techniques of relevance to chemists, life scientists and modellers working in drug discovery. The workshop group studies problems with hands-on examples using leading-edge software and discusses complex issues highlighted by examples and case studies presented by instructors. A variety of leading drug discovery software packages and an IT classroom are used by instructors and participants to work through problems. Bursary: A Bursary Award sponsored by Tripos will be used to support the attendance of one academic participant, who may be working in any area of research related to drug discovery. To apply for the bursary please send an email with a) description of your research (ca. 500 words); b) your training needs (ca. 500 words), c) your CV to echeminfo -[at]- douglasconnect.com by 15 April 2008. The recipient of the award will be selected based on an evaluation of the quality and innovation of the described research and the potential positive impact of the training on their research progress and will be notified by 30 April. We gratefully acknowledge the sponsorship support of Tripos. More Information: Web: http://echeminfo.colayer.net/COMTY_training Blog: http://barryhardy.blogs.com/cheminfostream best regards Barry Hardy eCheminfo Community of Practice Douglas Connect Switzerland Tel: +41 61 851 0170