From owner-chemistry@ccl.net Thu Jan 21 05:03:01 2010 From: "Serdar Bado?lu sbadoglu=gazi.edu.tr" To: CCL Subject: CCL: IR / Raman software Message-Id: <-41091-100121050049-2012-YpK7RNyHx3aM20g4Qj8CPA,+,server.ccl.net> X-Original-From: "Serdar Bado?lu" Date: Thu, 21 Jan 2010 10:00:29 -0000 Sent to CCL by: "Serdar Bado?lu" [sbadoglu!=!gazi.edu.tr] Hi CCLers, I'm looking for a software which can read and view IR and Raman spectra in well known formats (*.0, *.ras, *.sp, etc); must be capable of creating *.dpt style text files from the viewed spectrum ; prefarably freeware. Any suggestions? Regards. -- Serdar BADOGLU From owner-chemistry@ccl.net Thu Jan 21 08:55:00 2010 From: "Vincent Vivien vincent()eyesopen.com" To: CCL Subject: CCL:G: OpenEye EuroCUP IV - Apr 28-30, 2010 - Bergisch-Gladbach (Cologne) Message-Id: <-41092-100121035422-12045-mcAn6TjSpmTqBmqSIVIYng:+:server.ccl.net> X-Original-From: "Vincent Vivien" Date: Thu, 21 Jan 2010 03:54:18 -0500 Sent to CCL by: "Vincent Vivien" [vincent a eyesopen.com] Dear Colleague, The preliminary program for EuroCUP IV, OpenEye's 4th annual European science meeting, held this year in Bergisch-Gladbach (near Cologne) Germany on April 28-30, 2010, is now available. In addition to the 4 Main Sessions, we will have a half-day Toolkit Session where toolkit users will have the opportunity to share some of their work. A 2-day training course on Shape-based Virtual Screening will also be offered - see the Additional Information section for details. Below are the 4 main sessions and the already confirmed speakers: > Shape & Electrostatics > Physics-based modeling > Are proteins useful for drug discovery? > Ligand-based modeling rules Allocution: Jean-Louis Reymond, University of Berne: " Mining the Chemical Space for Drug Discovery". - Juergen Bajorath, University of Bonn - Kim Branson, Vertex Pharmaceuticals - Andreas Evers, Sanofi-Aventis Deutschland GmbH - Holger Gohlke, University of Duesseldorf - Andrew Grant, AstraZeneca UK - Neil Hales, AstraZeneca UK (retired) - Oliver Korb, Cambridge Crystallographic Data Centre - Hugo Kubinyi, University of Heidelberg and BASF (retired) - Richard Law, Evotec (UK) Ltd - F. Javier Luque, University of Barcelona - Steve Muchmore, Abbott Laboratories - Frederico Nardi, Sanofi-Aventis R&D - Jens Nielsen, University of Dublin - Peter Taylor, AstraZeneca UK (retired) There is a speaking slot still available, and there are also poster exhibitions. So if you would like to submit an abstract or simply join us please follow the link below to register. http://www.eyesopen.com/forms/eurocup4_reg.html **NOTE THAT YOU DO NOT NEED TO BE A CUSTOMER OF OPENEYE TO PARTICIPATE!** As always, except for the training, there is NO REGISRATION COST for the meeting. Attendees need only cover travel and accommodation. We very much hope you will be able to join us in Bergisch-Gladbach! With kind regards, Vincent Vivien Director of European Accounts Office: +33 389 589 544 vincent ~~ eyesopen.com www.eyesopen.com ADDITIONAL INFORMATION ---------------------- General Schedule ---------------- - Mon & Tue, April 26-27th (9am-6pm): Shape-Based Virtual Screening Training - Wed, April 28th (9:30am - 12:30pm): Toolkit Session - Wed, April 28th (3pm) to Fri, April 30th (12pm) EuroCUP IV Main Sessions Deadlines --------- - Abstract submission deadline for talks: January 31st, 2010 - Abstract submission deadline for posters: March 28th, 2010. - Registration deadline: March 28th, 2010. Because of the limited number of rooms available at the conference hotel however, it is likely that these will be filled well before that date. So please register early! Hotel ----- The location of the meeting and official hotel is the Schlosshotel Lerbach (http://www.schlosshotel-lerbach.com/en/home). You do NOT need to book the hotel yourself, OpenEye will make the reservation for you with the information you will provide in the registration form. Travel ------ Those flying will want to aim for Cologne-Bonn airport CGN: http://www.koeln-bonn-airport.de/index.php), which is only a 15-20-min taxi ride from to the hotel. Shape-Based Virtual Screening Training -------------------------------------- Virtual screening can be defined as any method that ranks a set of compounds by some score. In shape-based ligand-centric virtual screening, molecules are ranked on the basis of their similarity to a known active molecule in three-dimensional shape space, using atom-centered Gaussian functions to allow rapid maximization of molecular overlap. Who should attend: This workshop is geared toward new or intermediate users. Medicinal chemists and experienced modelers who are making the transition to OpenEye Scientific Software applications will also find this workshop invaluable. What you will learn: This is a hands-on workshop that focuses on good modeling practices and a step-by-step approach to ligand-based virtual screening. You will follow the standard virtual screening workflow and you will learn all the need-to-know stuff in a dynamic group setting. After you complete this workshop, you will be ready to tackle your own real-world ligand-based virtual screening problems. OpenEye Software Applications Used: EON, FILTER, OMEGA (with FLIPPER), QUACPAC, ROCS, VIDA, VIVANT. Costs and Payments ------------------ Except for the training, the cost only covers delegates' accommodation and full board. - Training on Shape-based Virtual Screening (2 nights / 2 days): 1100 USD (training registration fee) + 500 euros (accommodation and full board) - Toolkit Session (1 night / 0.5 day): 250 euros - Main EuroCUP IV Sessions (2 nights, 2 days): 550 euros Prepayment for the Shape-Based Virtual Screening training fee is required before the meeting. It can be made online by credit cards after verification > from the EuroCUP organizers (vincent ~~ eyesopen.com) that you are in the training session. Payments covering the Training accommodation, Toolkit session and Main EuroCUP IV sessions will be made directly to the hotel upon checkout, together with any incidentals, unless prior arrangement has been made with EuroCUP organizers. Please see the registration form for details of what's included, as well as pricing options for local delegates. Student Bursaries ----------------- A limited number of student bursaries are available for poster presentations. These will cover the costs associated with attendance to the Main EuroCUP IV Sessions, i.e. accommodation and full board. For consideration, please use the registration form to submit your poster abstract and use the comments field to precise that you are applying for a student bursary. From owner-chemistry@ccl.net Thu Jan 21 09:30:00 2010 From: "Mateusz Galuszka mateusz.galuszka_._selvita.com" To: CCL Subject: CCL: SPMP 2.0 -new release of Selvita Protein Modeling Platform Message-Id: <-41093-100121040054-12498-MrP5wa/v1F23WsCLRbxLFA-x-server.ccl.net> X-Original-From: "Mateusz Galuszka" Date: Thu, 21 Jan 2010 04:00:50 -0500 Sent to CCL by: "Mateusz Galuszka" [mateusz.galuszka~~selvita.com] Dear All, We are pleased to announce the release of a major new upgrade (version 2.0) of Selvita Protein Modeling Platform. Selvita (www.selvita.com) is a biotechnology company based in Krakow, Poland. One of the company's primary areas of expertise are Molecular Modeling and Computer Assisted Drug Design services & software design . SPMP 2.0 provides the necessary set of tools for protein structure and interactions modeling in web-based interface adapted for both beginner and expert users' needs. Selvita Protein Modeling Platform is based on CABS algorithm, created by Prof. Andrzej Kolinski, a world renowned expert in the field of protein structure modeling - a unique CASP competition-winning technology (1st place in CASP6 competition among over 200 competitors, see Debe et al. Proteins. 64(4):960-967, 2006) The new release features a new protein-protein/ protein-peptide docking module, usability enhancements, and improvement of discovery results for its users. The main features of SPMP 2.0 include: * Protein-protein/protein-peptide docking module (unprecedented, substantial degree of protein backbone flexibility) * Protein structure prediction at all levels of complexity (homology modeling, fold recognition, de novo folding) * Homology modeling using either single or many templates * BLAST sequence alignment and PSI-PRED secondary structure prediction * Superior prediction capabilities for difficult homology modeling and de novo cases compared to existing methods * A unique solution for antibodyantigen modeling (loop modeling combined with docking protocol) * Integration with GROMACS - a versatile and very well optimized package for molecular simulation * Cross platform web based GUI (requires only java enabled web browser and java runtime environment) * Fully-automated selection of modeling route (alternatively: access to all the settings) SPMP is a tool for both newbies and gurus. * Possibility of protein structure prediction using in-silico modeling combined with the use of sparse experimental data (NMR) for improved model accuracy. Please visit our website http://www.selvita.com/selvita-protein-modeling-platform.html to find out more about our technology and applications. In case of any questions please feel free to ask us. We are also looking for possible scientific collaborations regarding the development of our platform. If you would be interested in such partnership, please do not hesitate to contact us. Best regards, -- Mateusz Galuszka Product Manager - Bioinformatics Selvita sp. z o.o. ul. Ostatnia 1c, 31-444 Krakow, Poland tel.: +48 12 41 07 380 mobile +48 666 331 923 fax: +48 12 410 73 82 e-mail: mateusz.galuszka::selvita.com www: http://www.selvita.com From owner-chemistry@ccl.net Thu Jan 21 10:50:01 2010 From: "Michael Boruta michael.boruta*o*acdlabs.com" To: CCL Subject: CCL: IR / Raman software Message-Id: <-41094-100121084403-3121-59G+DNnuzv/WVZ3Bmt9D9A]|[server.ccl.net> X-Original-From: "Michael Boruta" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Thu, 21 Jan 2010 07:43:50 -0500 MIME-Version: 1.0 Sent to CCL by: "Michael Boruta" [michael.boruta::acdlabs.com] Dear Serdar, ACD/Labs has software that can read most instrument and common formats and output a txt file. For the specific file formats you listed; .0 Bruker - we can read .ras Unsure what this format is. .spc galactic - we can read. I'm not sure what a .dtp file is so I cannot comment directly about that format, but we can create an ASCII text file. Our software is not free - however we do discount for academia. I believe the discount is about 75%. You can get more information about the software by visiting our website at http://www.acdlabs.com/products/spec_lab/exp_spectra/uv_ir/proc.html Hope this is helpful. Sincerely, Michael Boruta Optical Spectroscopy Product Manager Advanced Chemistry Development, Inc. (ACD/Labs) 110 Yonge Street, 14th floor Toronto ON M5C 1T4 Canada T: 215 357 8855=20 F: 253 540 2940 Cell phone: 267 303 3809 Toll Free 1-800-304-3988 michael.boruta]|[acdlabs.com www.acdlabs.com =20 CONFIDENTIALITY NOTICE Unless expressly stated otherwise, this message is confidential and is intended for the addressee(s) only. If you are not an addressee, please inform the sender immediately or contact info]|[acdlabs.com. -----Original Message----- > From: owner-chemistry+michael.boruta=3D=3Dacdlabs.com]|[ccl.net [mailto:owner-chemistry+michael.boruta=3D=3Dacdlabs.com]|[ccl.net] On = Behalf Of Serdar Bado?lu sbadoglu=3Dgazi.edu.tr Sent: Thursday, January 21, 2010 5:00 AM To: Michael Boruta Subject: CCL: IR / Raman software Sent to CCL by: "Serdar Bado?lu" [sbadoglu!=3D!gazi.edu.tr] Hi CCLers, I'm looking for a software which can read and view IR and Raman spectra in well known formats (*.0, *.ras, *.sp, etc); must be capable of creating *.dpt style text files from the viewed spectrum ; prefarably freeware. Any suggestions? Regards. --=20 Serdar BADOGLU -=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 21 14:43:00 2010 From: "mhmd T. aish mhmdaish*yahoo.com" To: CCL Subject: CCL:G: fluorescent enhancement and quenching Message-Id: <-41095-100121144202-8583-nq+HtoafNJs8COnwPoHZuA===server.ccl.net> X-Original-From: "mhmd T. aish" Date: Thu, 21 Jan 2010 14:41:58 -0500 Sent to CCL by: "mhmd T. aish" [mhmdaish###yahoo.com] Dear CCls I am wandering about the differences between the fluorescent enhancement and quenching and how can we differentiate between them using TDDFT (G03 and ADF). I have another question and dont know if this question has a relation with the previous one or not: is there any benefit of the oscillator strength value, in other words, this value could be attributed to the strength of fluorescence intensity, so, can we use it to judge on the enhancement or quenching? I will be very appreciated for your answering. Best Regards