From goetz_stefan at gmx.de Thu Jul 9 09:16:41 2009 From: goetz_stefan at gmx.de (=?iso-8859-1?Q?=22Stefan_G=F6tz=22?=) Date: Thu, 09 Jul 2009 15:16:41 +0200 Subject: [BiO BB] Blast2GO announces: First international course in automated functional annotation and data-mining Message-ID: <20090709131641.207940@gmx.net> Dear Colleagues, We are very pleased to announce a first international course in automated functional annotation and data-mining. The course will provide know-how and bioinformatics resources to assigning rich functional labels to high-dimensional sequence datasets and to extract new knowledge from annotation data. In this course you will learn tools and tips for functional annotation, visualization and analysis of novel sequence data making use of Blast2GO. The course will be offered to 35 participants at 2 locations: - Valencia, Spain: 28 to 30, September 2009 - Florida, USA: 14 to 16, October, 2009 For more information and registration until the 1 of September please visit: http://bioinfo.cipf.es/blast2gocourse With best regards, Ana Conesa and Stefan G?tz -------------------------------------------- Stefan G?tz Bioinformatics Department Centro de Investigaci?n Pr?ncipe Felipe (CIPF) C/E.P. Avda. Autopista del Saler, 16-3 (junto Oceanogr?fico) 46013 Valencia, Spain Tel: +34 963289680 Ext. 1011 Fax: +34 963289574 E-Mail: sgoetz at cipf.es http://bioinfo.cipf.es -------------------------------------------- -- GRATIS f?r alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01 From s.park at ks3.ecs.kyoto-u.ac.jp Fri Jul 10 00:04:26 2009 From: s.park at ks3.ecs.kyoto-u.ac.jp (Sung-Joon Park) Date: Fri, 10 Jul 2009 13:04:26 +0900 Subject: [BiO BB] GIW 2009 CFP - Pacifico Yokohama, Japan, December 14-16, 2009 Message-ID: <1247198666434356.1880400283@mail4.ecs.kyoto-u.ac.jp> The Twentieth International Conference on Genome Informatics (GIW 2009) (20th anniversary) December 14-16, 2009 Pacifico Yokohama, Japan ( http://giw.ims.u-tokyo.ac.jp/giw2009/ ) [TOPICS] Genome Informatics Workshop (GIW) is the longest running international bioinformatics conference, which has provided unique opportunities that bridge theory and experiments, academia and industry, and East and West. This year's GIW is the 20th anniversary. The scope includes all work that is ultimately devoted to the computational understanding of biological systems on a molecular basis and the aims are to present recent results of both theoretical and practical research, to show new applications, to demonstrate systems, and to indicate directions of future research. [SPONSORS] Japanese Society for Bioinformatics (JSBi) Human Genome Center, Institute of Medical Science, University of Tokyo [PAPER SUBMISSION GUIDELINES] http://giw.ims.u-tokyo.ac.jp/giw2009/instructions_for_authors.html http://giw.ims.u-tokyo.ac.jp/giw2009/paper/submit/ http://giw.ims.u-tokyo.ac.jp/giw2009/poster/submit/ [PAPER DEADLINES] July 26 (11:59pm Japan Standard Time), 2009 - Submission deadline August 19, 2009 - Notification of acceptance/rejection August 31, 2009 - Camera ready due [POSTER/DEMO DEADLINES] October 1, 2009 - Poster/Demo submission deadline October 21, 2009 - Notification of acceptance/rejection Several posters will be selected for short oral presentations. [QUESTIONS] Yasubumi Sakakibara (Conference Chair) Email: giw2009 at ims.u-tokyo.ac.jp Human Genome Center, Institute of Medical Science, University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan [PUBLICATION] Accepted papers will be published in "Genome Informatics Vol.23" from Imperial College Press. Genome Informatics Series is MEDLINE indexed. Abstracts of accepted posters and software demonstrations are not included in "Genome Informatics Vol.23". [KEYNOTE SPEAKERS] Confirmed keynote speakers: Sean Eddy, HHMI's Janelia Farm, USA Minoru Kanehisa, Kyoto University, Japan Sang Yup Lee, KAIST, Korea Hideyuki Okano, Keio University, Japan Mark Ragan, University of Queensland, Australia [PROGRAM COMMITTEE] Shin-ichi Morishita, University of Tokyo, Japan (PC Co-Chair) Sang Yup Lee, KAIST, Korea (PC Co-Chair) Cathy Abbott, Flinders University, Australia Jonathan Arthur, University of Sydney, Australia Vladimir Bajic, SANBI, South Africa Christopher Baker, Institute for Infocomm Research, Singapore Guillaume Bourque, Genome Institute of Singapore, Singapore Jung-Hsien Chiang, National Cheng Kung University, Taiwan Francis Chin, The University of Hong Kong, Hong Kong Peter Clote, Boston College, USA Aaron Darling, University of Queensland, Australia Bhaskar DasGupta, University of Illinois, USA Colin Dewey, University of Wisconsin, USA Chris Ding, University Texas at Arlington, USA Wen-Lian Hsu, Academia Sinica, Taiwan Seiya Imoto, University of Tokyo, Japan Minoru Kanehisa, Kyoto University, Japan Uri Keich, Cornell University, USA Daisuke Kihara, Purdue University, USA Dong-Yup Lee, Bioprocessing Institute & National University of Singapore, Singapore Ming Li, University of Waterloo, Canada Frederique Lisacek, Swiss Institute of Bioinformatics, Switzerland Hiroshi Mamitsuka, Kyoto University, Japan Aleksandar Milosavljevic, Baylor College of Medicine, USA Satoru Miyano, University of Tokyo, Japan Bernard Moret, Swiss Federal Institute of Technology, Switzerland Akihiro Nakaya, University of Tokyo, Japan See-Kiong Ng, Institute for Infocomm Research, Singapore William Noble, University of Washington, USA Laxmi Parida, IBM T.J. Watson Research Center, USA Ron Pinter, Technion, Israel Shoba Ranganathan, Macquarie University, Australia Rintaro Saito, Keio University, Japan Christian Schoenbach, Nanyang Technological University, Singapore Tetsuo Shibuya, University of Tokyo, Japan Mona Singh, Princeton University, USA Wing-Kin Sung, National University of Singapore, Singapore Koji Tsuda, Max Planck Institute for Biological Cybernetics, Germany Gabriel Valiente, Technical University of Catalonia, Spain Lusheng Wang, The City University of Hong Kong, Hong Kong Gwan-Su Yi, Information and Communication University, Korea Mohammed Zaki, Rensselaer Polytechnic Institute, USA From deep_kumar at imtech.res.in Sun Jul 12 13:40:35 2009 From: deep_kumar at imtech.res.in (deep_kumar at imtech.res.in) Date: Sun, 12 Jul 2009 23:10:35 +0530 (IST) Subject: [BiO BB] paper Message-ID: <37180.59.160.112.43.1247420435.squirrel@webmail.imtech.res.in> we have published a paper on hormone receptor database.hopefully it will be useful to you.i am providinf the url of it. http://www.biomedcentral.com/1471-2164/10/307 if you are using this database.please cite this paper. deepak From ngadewal at yahoo.com Fri Jul 17 02:33:54 2009 From: ngadewal at yahoo.com (nikhil gadewal) Date: Thu, 16 Jul 2009 23:33:54 -0700 (PDT) Subject: [BiO BB] size of cavity Message-ID: <301248.90920.qm@web51511.mail.re2.yahoo.com> Dear all, ? I am looking for the online tool or program to calculate the volume of the cavity in a given protein structure. Thanks & regards, ? NIKHIL S. GADEWAL ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, India From tanasa at gmail.com Fri Jul 17 14:24:27 2009 From: tanasa at gmail.com (Bogdan Tanasa) Date: Fri, 17 Jul 2009 11:24:27 -0700 Subject: [BiO BB] miRNA enrichment Message-ID: <47d9979f0907171124y3e532f94r5de19a535b9ae36d@mail.gmail.com> Hello all, please could you let me know whether there is a software that calculates the enrichment in miRNA target sequences in a set of mRNA sequences ? much thanks, bogdan From clements at nescent.org Fri Jul 17 23:58:11 2009 From: clements at nescent.org (Dave Clements) Date: Fri, 17 Jul 2009 23:58:11 -0400 Subject: [BiO BB] GMOD Community Meeting, 6-7 August, 2009, Oxford UK Message-ID: There will be a GMOD Community Meeting, 6-7 August, 2009 at the University of Oxford, in Oxford, UK. GMOD (http://gmod.org) is a collection of interoperable, open-source software components for managing, visualizing, annotating, and sharing biological data. GMOD is also a community of users and developers addressing common challenges with their biological data. The popularity of next generation sequencing and other high-throughput methods has made this GMOD meeting particularly timely. GMOD meetings are an excellent opportunity to learn best practices from other researchers, to meet GMOD users and developers, and to learn and affect what is coming in the project. As with previous meetings, there will be a mixture of project talks, component-focused talks, and user talks. Registration for the meeting is now open and space is available on a first come, first served basis. Attendance is limited to the first 55 people to register. The meeting cost is ?50. See http://gmod.org/wiki/August_2009_GMOD_Meeting to register for more. Please join us in Oxford this August. Cheers, Dave Clements GMOD Help Desk -- Register now for the August GMOD Meeting: http://gmod.org/wiki/August_2009_GMOD_Meeting From marchywka at hotmail.com Mon Jul 20 17:34:51 2009 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 20 Jul 2009 17:34:51 -0400 Subject: [BiO BB] size of cavity In-Reply-To: <301248.90920.qm@web51511.mail.re2.yahoo.com> References: <301248.90920.qm@web51511.mail.re2.yahoo.com> Message-ID: ---------------------------------------- > Date: Thu, 16 Jul 2009 23:33:54 -0700 > From: ngadewal at yahoo.com > To: bbb at bioinformatics.org > Subject: [BiO BB] size of cavity > > Dear all, > > I am looking for the online tool or program to calculate the volume of the cavity in a given protein structure. > I don't know about online but if you can't find what you need and can play with a glut demo program, I've used this for outlining cavities, http://www.spottext.com/marchywka/glutp/docs_surfaces.html shouldn't be hard to find volume. Also try a search on wikipedia.org, they have some good "list of molecular related software" pages. > Thanks & regards, > > NIKHIL S. GADEWAL > ACTREC, > Tata Memorial Centre, > Kharghar, > Navi Mumbai, > India > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Windows Live? SkyDrive?: Store, access, and share your photos. See how. http://windowslive.com/Online/SkyDrive?ocid=TXT_TAGLM_WL_CS_SD_photos_072009 From dan.bolser at gmail.com Mon Jul 20 17:38:26 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 20 Jul 2009 22:38:26 +0100 Subject: [BiO BB] size of cavity In-Reply-To: References: <301248.90920.qm@web51511.mail.re2.yahoo.com> Message-ID: <2c8757af0907201438y6b0c3330t4eb87afcef1abf77@mail.gmail.com> You could try asking on PDB-L I keep a list of mailing lists here: http://biodatabase.org/index.php/List_of_mailing_lists_for_biologists Dan. 2009/7/20 Mike Marchywka : > > ---------------------------------------- >> Date: Thu, 16 Jul 2009 23:33:54 -0700 >> From: ngadewal at yahoo.com >> To: bbb at bioinformatics.org >> Subject: [BiO BB] size of cavity >> >> Dear all, >> >> I am looking for the online tool or program to calculate the volume of the cavity in a given protein structure. >> > > I don't know about online but if you can't find what you need and can > play with a glut demo program, I've used this for outlining cavities, > > http://www.spottext.com/marchywka/glutp/docs_surfaces.html > > shouldn't be hard to find volume. ?Also try a search on wikipedia.org, > they have some good "list of molecular related software" pages. > >> Thanks & regards, >> >> NIKHIL S. GADEWAL >> ACTREC, >> Tata Memorial Centre, >> Kharghar, >> Navi Mumbai, >> India From ppkarthikeyan at gmail.com Tue Jul 21 01:27:29 2009 From: ppkarthikeyan at gmail.com (P.P.Karthi keyan) Date: Tue, 21 Jul 2009 10:57:29 +0530 Subject: [BiO BB] size of cavity In-Reply-To: <2c8757af0907201438y6b0c3330t4eb87afcef1abf77@mail.gmail.com> References: <301248.90920.qm@web51511.mail.re2.yahoo.com> <2c8757af0907201438y6b0c3330t4eb87afcef1abf77@mail.gmail.com> Message-ID: <4f34e5840907202227w76fcc8ceiac952488372131de@mail.gmail.com> Hi ! U may try the QSITE FINDER - http://www.modelling.leeds.ac.uk/pocketfinder/ CASTP -http://sts-fw.bioengr.uic.edu/castp/calculation.php This help in predicting the active site cavity area... Thanking you, regards, P.P.Karthikeyan. ------------------ P.P.Karthikeyan, http://ppkarthikeyan.googlepages.com/ http://iscbsc.org/rsg/rsg-india/ 2009/7/21 Dan Bolser > You could try asking on PDB-L > > > I keep a list of mailing lists here: > > http://biodatabase.org/index.php/List_of_mailing_lists_for_biologists > > > Dan. > > 2009/7/20 Mike Marchywka : > > > > ---------------------------------------- > >> Date: Thu, 16 Jul 2009 23:33:54 -0700 > >> From: ngadewal at yahoo.com > >> To: bbb at bioinformatics.org > >> Subject: [BiO BB] size of cavity > >> > >> Dear all, > >> > >> I am looking for the online tool or program to calculate the volume of > the cavity in a given protein structure. > >> > > > > I don't know about online but if you can't find what you need and can > > play with a glut demo program, I've used this for outlining cavities, > > > > http://www.spottext.com/marchywka/glutp/docs_surfaces.html > > > > shouldn't be hard to find volume. Also try a search on wikipedia.org, > > they have some good "list of molecular related software" pages. > > > >> Thanks & regards, > >> > >> NIKHIL S. GADEWAL > >> ACTREC, > >> Tata Memorial Centre, > >> Kharghar, > >> Navi Mumbai, > >> India > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From mourad12345678 at yahoo.com Tue Jul 21 19:53:56 2009 From: mourad12345678 at yahoo.com (Mourad Elloumi) Date: Tue, 21 Jul 2009 16:53:56 -0700 (PDT) Subject: [BiO BB] CfP: ACS/IEEE Int'l Conf. on Computer Systems & Applications (Hammamet, Tunisia) Message-ID: <599889.3918.qm@web31504.mail.mud.yahoo.com> ??????????????????????????????????? Call for Papers ????????????? 2010 ACS/IEEE International Conference on ????????????????????Computer Systems and Applications ???????????????????????????? HAMMAMET, TUNISIA ???????????????????????????????? May 16-19th, 2010 ???????????????????????????????????? http://www2.lifl.fr/AICCSA2010/ ? ??????????????http://www2.lifl.fr/AICCSA2010/index.php?n=Main.ProgramCommittee ? The eighth ACS/IEEE International Conference on Computer Systems and Applications (AICCSA-10) will be held in Hammamet, Tunisia in May 2010. AICCSA is the first Computer Science and Engineering Conference in the Middle East and North Africa. Authors are invited to submit papers describing new advances in computer systems and their applications. We welcome papers that are theoretical, conceptual, descriptive in nature, or a survey of the state of the art. The official language for the conference is English. Topics of interest include, but are not limited to Algorithms and Bioinformatics Computer Architecture and Real Time Systems Database and Data Mining DSP/Image Processing/Pattern Recognition/Multimedia Geographical Information Systems/ Global Navigation Satellite Systems Modeling and Simulation Networking and Telecommunications Parallel and Distributed Systems Security and Information Assurance Soft Computing (AI, Neural networks, Fuzzy Systems, etc.) Software engineering Important due dates Paper and Poster Submissions: October 13, 2009 (Firm)-11:59 pm (EST) Workshop, Tutorial and Panel Submissions: October 13, 2009 (Firm)-11:59 pm (EST) Notification of acceptance: December 19, 2009 Camera ready copy due: February 5, 2010 Author Registration: February 5, 2010 From vipin.skb at gmail.com Wed Jul 29 09:24:12 2009 From: vipin.skb at gmail.com (VIPIN THOMAS) Date: Wed, 29 Jul 2009 18:54:12 +0530 Subject: [BiO BB] Molecular Simulation tool Message-ID: <8284f78f0907290624wc398e01tf04ffe9e2a59235e@mail.gmail.com> Hi, Can anyone suggest me a simulation tool, preferably a freeware, with features like structure refinement, energy minimisation and dynamics simulations. Thanks in advance VIPIN -- VIPIN THOMAS Nila, Techno Park Thiruvananthapuram INDIA- 695 581 www.sooryakiran.com Ph: 91-9895429350 From dan.bolser at gmail.com Thu Jul 30 03:53:38 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 30 Jul 2009 08:53:38 +0100 Subject: [BiO BB] Molecular Simulation tool In-Reply-To: <8284f78f0907290624wc398e01tf04ffe9e2a59235e@mail.gmail.com> References: <8284f78f0907290624wc398e01tf04ffe9e2a59235e@mail.gmail.com> Message-ID: <2c8757af0907300053w1ccbe228k1010867e6d5e011@mail.gmail.com> 2009/7/29 VIPIN THOMAS : > Hi, > > Can anyone suggest me a simulation tool, preferably a freeware, with > features like structure refinement, energy minimisation and dynamics > simulations. I think Yasara does at least some of these things. http://www.yasara.org/ It's not free as in FLOSS, but the 'basic' features won't cost you anything :-) > Thanks in advance > VIPIN > > -- > VIPIN THOMAS > Nila, Techno Park > Thiruvananthapuram > INDIA- 695 581 > www.sooryakiran.com > Ph: 91-9895429350 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From marchywka at hotmail.com Thu Jul 30 06:23:12 2009 From: marchywka at hotmail.com (Mike Marchywka) Date: Thu, 30 Jul 2009 06:23:12 -0400 Subject: [BiO BB] Molecular Simulation tool In-Reply-To: <2c8757af0907300053w1ccbe228k1010867e6d5e011@mail.gmail.com> References: <8284f78f0907290624wc398e01tf04ffe9e2a59235e@mail.gmail.com> <2c8757af0907300053w1ccbe228k1010867e6d5e011@mail.gmail.com> Message-ID: > 2009/7/29 VIPIN THOMAS : >> Hi, >> >> Can anyone suggest me a simulation tool, preferably a freeware, with >> features like structure refinement, energy minimisation and dynamics >> simulations. > > I think Yasara does at least some of these things. http://www.yasara.org/ > > It's not free as in FLOSS, but the 'basic' features won't cost you anything :-) Actually, what may be of interest is an open source SDK or related library for MD simulations. Phrased this way, any other options come to mind? I've thought about playing with some simple cases myself for either biological or semiconductor interest but never bothered to try anything out. Wikipedia often times has good entries. There is a list of things here with links etc, http://en.wikipedia.org/wiki/Molecular_dynamics ( or use google confined to wikipedia.org ) I haven't checked sourceforge or looked for libraries on google but may be worth a try. Also, you can check papers from people active in related fields http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=molecular+dynamics+simulation and see if anything seems helpful and contact authors. > > >> Thanks in advance >> VIPIN >> >> -- >> VIPIN THOMAS >> Nila, Techno Park >> Thiruvananthapuram >> INDIA- 695 581 Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 415-264-8477 (w)<- use this 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: hotmail is getting cumbersom, try also marchywka at yahoo.com _________________________________________________________________ NEW mobile Hotmail. Optimized for YOUR phone. Click here. http://windowslive.com/Mobile?ocid=TXT_TAGLM_WL_CS_MB_new_hotmail_072009 From lijo.skb at gmail.com Thu Jul 30 02:18:59 2009 From: lijo.skb at gmail.com (Lijo) Date: Wed, 29 Jul 2009 23:18:59 -0700 Subject: [BiO BB] Molecular Simulation tool In-Reply-To: <8284f78f0907290624wc398e01tf04ffe9e2a59235e@mail.gmail.com> References: <8284f78f0907290624wc398e01tf04ffe9e2a59235e@mail.gmail.com> Message-ID: vipin, have you tried Gromac(don't know available in windows)? may be you can check with NAMD too for your purpose? lijo On Wed, Jul 29, 2009 at 6:24 AM, VIPIN THOMAS wrote: > Hi, > > Can anyone suggest me a simulation tool, preferably a freeware, with > features like structure refinement, energy minimisation and dynamics > simulations. > > Thanks in advance > VIPIN > > -- > VIPIN THOMAS > Nila, Techno Park > Thiruvananthapuram > INDIA- 695 581 > www.sooryakiran.com > Ph: 91-9895429350 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Centre for Bioinformatics, University of Kerala, India. +91 9446515705 From skhadar at gmail.com Thu Jul 30 03:19:30 2009 From: skhadar at gmail.com (Shameer Khadar) Date: Thu, 30 Jul 2009 12:49:30 +0530 Subject: [BiO BB] Molecular Simulation tool In-Reply-To: <8284f78f0907290624wc398e01tf04ffe9e2a59235e@mail.gmail.com> References: <8284f78f0907290624wc398e01tf04ffe9e2a59235e@mail.gmail.com> Message-ID: Gromacs is your best friend or NAMD for sure. Cheers, K. Shameer NCBS - TIFR On Wed, Jul 29, 2009 at 6:54 PM, VIPIN THOMAS wrote: > Hi, > > Can anyone suggest me a simulation tool, preferably a freeware, with > features like structure refinement, energy minimisation and dynamics > simulations. > > Thanks in advance > VIPIN > > -- > VIPIN THOMAS > Nila, Techno Park > Thiruvananthapuram > INDIA- 695 581 > www.sooryakiran.com > Ph: 91-9895429350 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From andrea.bazzoli at unimi.it Thu Jul 30 03:34:27 2009 From: andrea.bazzoli at unimi.it (Andrea Bazzoli) Date: Thu, 30 Jul 2009 09:34:27 +0200 Subject: [BiO BB] Molecular Simulation tool In-Reply-To: <8284f78f0907290624wc398e01tf04ffe9e2a59235e@mail.gmail.com> References: <8284f78f0907290624wc398e01tf04ffe9e2a59235e@mail.gmail.com> Message-ID: Hi Vipin, you can try GROMACS (http://www.gromacs.org/) for molecular dynamics and energy minimization, and MODELLER (http://salilab.org/modeller/) for structural refinement. Andrea ----- Messaggio Originale ----- Da: VIPIN THOMAS Data: Giovedi', Luglio 30, 2009 3:40 am Oggetto: [BiO BB] Molecular Simulation tool A: bbb at bioinformatics.org > Hi, > > Can anyone suggest me a simulation tool, preferably a freeware, with > features like structure refinement, energy minimisation and dynamics > simulations. > > Thanks in advance > VIPIN > > -- > VIPIN THOMAS > Nila, Techno Park > Thiruvananthapuram > INDIA- 695 581 > www.sooryakiran.com > Ph: 91-9895429350 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From ana_zhu at hotmail.com Thu Jul 30 03:59:17 2009 From: ana_zhu at hotmail.com (ana_zhu at hotmail.com) Date: Thu, 30 Jul 2009 08:59:17 +0100 Subject: [BiO BB] Molecular Simulation tool In-Reply-To: <8284f78f0907290624wc398e01tf04ffe9e2a59235e@mail.gmail.com> References: <8284f78f0907290624wc398e01tf04ffe9e2a59235e@mail.gmail.com> Message-ID: Hi Coot is a good one. Cheers, Ana -------------------------------------------------- From: "VIPIN THOMAS" Sent: Wednesday, July 29, 2009 2:24 PM To: Subject: [BiO BB] Molecular Simulation tool > Hi, > > Can anyone suggest me a simulation tool, preferably a freeware, with > features like structure refinement, energy minimisation and dynamics > simulations. > > Thanks in advance > VIPIN > > -- > VIPIN THOMAS > Nila, Techno Park > Thiruvananthapuram > INDIA- 695 581 > www.sooryakiran.com > Ph: 91-9895429350 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From harry.mangalam at uci.edu Thu Jul 30 14:50:12 2009 From: harry.mangalam at uci.edu (Harry Mangalam) Date: Thu, 30 Jul 2009 11:50:12 -0700 Subject: [BiO BB] Molecular Simulation tool In-Reply-To: References: <8284f78f0907290624wc398e01tf04ffe9e2a59235e@mail.gmail.com> Message-ID: <200907301150.12389.harry.mangalam@uci.edu> Especially if you have a compatible Graphics card, the Zephyr app (https://simtk.org/home/zephyr) is GPGPU-enabled with very good speedups for some approaches. Uses VMD & Gromacs. versions for Win/Lin/Mac hjm On Thursday 30 July 2009 00:19:30 Shameer Khadar wrote: > Gromacs is your best friend or NAMD for sure. > > Cheers, > K. Shameer > NCBS - TIFR > > On Wed, Jul 29, 2009 at 6:54 PM, VIPIN THOMAS wrote: > > Hi, > > > > Can anyone suggest me a simulation tool, preferably a freeware, with > > features like structure refinement, energy minimisation and dynamics > > simulations. > > > > Thanks in advance > > VIPIN > > > > -- > > VIPIN THOMAS > > Nila, Techno Park > > Thiruvananthapuram > > INDIA- 695 581 > > www.sooryakiran.com > > Ph: 91-9895429350 > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb -- Harry Mangalam - Research Computing, NACS, Rm 225 MSTB, UC Irvine [ZOT 2225] / 92697 949 824-0084(o), 949 285-4487(c) MSTB=Bldg 415 (G-5 on --- pedalogogues: people who insist on riding bicycles to work and expect you to also. -karen lyons kalmenson- And yes, I am one.