From chemistry-request@www.ccl.net Fri Oct 31 13:55 EST 1997 Date: Fri, 31 Oct 1997 10:03:48 -0800 From: David Case To: amber@cgl.ucsf.edu, chemistry@www.ccl.net Subject: CCL:Announce: Amber 5.0 is available It gives us great pleasure to announce the release of AMBER 5.0. This code is a joint effort of the Kollman group at UCSF, the Case group at The Scripps Research Institute, David Pearlman at Vertex, the Merz group at Pennsylvania State University, Tom Darden at NIEHS, and David Ferguson at the University of Minnesota. As in the past, this version of AMBER will be jointly supported by Oxford Molecular (OM) as well as by the various authors. Oxford Molecular will offer commercial-level support and update services and the option of bundling AMBER with their other complementary software. AMBER 5.0 (1997) represents a significant change from the most recent previous version, 4.1, which was released in 1995. Briefly, the major differences include: (1) an updated and parallelized implementation of the particle-mesh Ewald routine, and its incorporation into the free energy module; (2) "locally-enhanced sampling" (LES) code that allows parts of the system to be present as multiple copies; (3) an alternate version of Sander (ROAR) that includes the ability to define part of the system as a quantum-mechanical section (QM/MM), and includes alternate integrators; (4) PROFEC (pictorial representation of free energy changes), a set of tools for carrying out and displaying extrapolative free energy changes; (5) new and parallelized methods for NMR refinement; incorporation of penalites based on pseudocontact shifts. (6) updates to the functionality and stability of LEaP. If you are interested in obtaining a copy of AMBER 5.0, please contact Oxford Molecular at one of the following sites: USA: Toll Free: 1-800-876-9994 phone (408) 879-6300 fax (408) 879-6302 e-mail: products@oxmol.com UK: phone +44 1865 784600 fax +44 1865 784601 e-mail: products@oxmol.co.uk Thank you for your interest and continued support. ========================================= From owner-chemweb@ic.ac.uk Tue Nov 25 06:21 EST 1997 Message-Id: Mime-Version: 1.0 Content-Transfer-Encoding: quoted-printable Date: Tue, 25 Nov 1997 11:17:14 -0500 To: Editor - Scitech Journal From: Andrew Lloyd Subject: Oxford Molecular Releases AMBER 5.0 Sender: owner-chemweb@ic.ac.uk Precedence: bulk Reply-To: Andrew Lloyd Content-Type: text/plain; charset="iso-8859-1" Oxford Molecular Releases AMBER=81 5.0 Photograph available Oxford, 25 November 1997 - Oxford Molecular Group, PLC (London Stock Exchange: OMG) announces the release of AMBER 5.0, a program for simulating peptide, protein and DNA structures and their interactions. AMBER, installed at more than 300 sites worldwide, is a highly respected set of simulation tools used by many major pharmaceutical companies as part of their drug discovery process. Oxford Molecular, in addition to investing money in AMBER development, has an exclusive co-distribution agreement with the University of California San Francisco (UCSF) and provides professional distribution, maintenance and installation support. AMBER 5.0 includes many significant enhancements that expand the range of problems that can be addressed. In addition, many functions have been parallelized to speed up the calculation process. Among the new capabilities of AMBER 5.0 are: PROFEC (pictorial representation of free energy changes) can play a role in the optimization of lead compounds in drug design, by rapidly screening the free energy effects of modifying chemical groups to look for improved binding. The realism of simulations of solvated DNA and protein/DNA are improved in the new parallelized implementation of the particle-mesh Ewald routine. For the first time, stable simulations can be carried out without artificial constraints. Enzyme reaction mechanisms, which involve bond-breaking processes, and unusual cofactors or metals, can now be addressed by incorporating a quantum mechanical description of an active site. Other enhancements include new parallelized methods for determining protein and nucleic acid structures from NMR data; these methods apply to paramagnetic metallo-enzymes as well as diamagnetic systems. The use of locally enhanced sampling in dynamics simulations can determine global energy minima of solvated systems in a viable fashion. AMBER 5.0 was produced through collaborative work among leading scientists. The team responsible for the development includes the Kollman Group at UCSF, the Case Group at The Scripps Research Institute, David Pearlman at Vertex, the Merz Group at Pennsylvania State University, Tom Darden at NIEHS and David Ferguson at the University of Minnesota. Professor Kollman of UCSF is a member of Oxford Molecular's Senior Scientific Advisory Board. - ends - For further information please contact: UK US Tony Marchington, D.Phil. Suzanne Mattingly, Ph.D. Chief Executive Officer or Vice President, Global Marketing Professor David Jackson Oxford Molecular Group, Inc. Chief Operating Officer Tel: +1 408 879 6300 Oxford Molecular Group, PLC Tel: +44 1865 784600 Andrew Lloyd Andrew Lloyd & Associates Ltd Tel: +44 1273 675100 Notes to Editors About Oxford Molecular Oxford Molecular is a worldwide provider of solutions for discovery research to chemical, pharmaceutical and biotechnology companies and universities. Using the company's wide range of computer-aided molecular design (CAMD) software, advanced bioinformatics tools, cheminformatics solutions and collaborative research services, researchers can reduce both cost and time, expediting discovery across multiple disciplines. Oxford Molecular has strategic alliances with Glaxo Wellcome, Yamanouchi Pharmaceutical Co., Silicon Graphics, Inc. and Digital Equipment Corporation, among others. It is the largest supplier of CAMD software in Japan through its distributor Sony/Tektronix. In addition, Teijin Systems Technology, Ltd., distributes Oxford Molecular's bioinformatics products and Fujitsu distributes its RS3 Discovery software for the management of research information. Oxford Molecular has headquarters in Oxford, England and operations in Erlangen (Germany). US offices are in: Campbell, California; Beaverton, Oregon; Rochester, New York; Towson, Maryland; South San Francisco, California; and Madison, Wisconsin. For product information, please call: US, toll-free: 1-800-876-9994; UK: +44 1865 784600 Web site addresses: http://www.oxmol.com : http://www.oxmol.co.uk Brighton Business Centre 221 bd Raspail 95 Ditchling Road 75014 Paris Brighton BN1 4ST France England Tel: +44-1273 675100 Tel: +33-1 43 22 79 56 Fax: +44-1273 675400 Fax: +33-1 43 20 90 92 email: allo@ala.com OR ala-france@ala.com (For ALA Paris office only) OR ala@pavilion.co.uk (For ALA UK office only) INTERNATIONAL TECHNOLOGY MARKETS STRATEGY & COMMUNICATIONS