Accelrys Announces DS Modeling 1.1: First Discovery Studio(TM) X-Ray Tools for Target Characterization

Posted on July 30, 2003 By Corinne Jones News

San Diego, CA, July 30 2003

Accelrys Inc., a wholly owned subsidiary of Pharmacopeia, Inc. (NASDAQ: PCOP), today announced its newest applications for the Discovery Studio(TM) family of products slated for commercial release in Fall 2003. DS Modeling 1.1 is a client-server environment for in silico modeling and simulation research on Windows(R)-based personal computers. Its high quality graphics, well-validated science, and eResearch tools facilitate protein target characterization using X-ray crystallography and homology modeling.

DS Modeling 1.1 is the first Discovery Studio product to integrate functionality from both the QUANTA(R) suite of crystallographic modeling tools and the Insight II(R) 3D graphical environment for molecular modeling and simulation. DS Modeling 1.1 also features integrated, easy-to-use tools, including an experimental wizard, to guide researchers through set-up and running of experiments, ultimately enabling them to make better informed decisions based on validated, well-established science.

Coupled with DS ProjectKM, an Oracle(R) relational database, DS Modeling 1.1 helps track the progress of experimental and in silico results. DS Modeling 1.1 integrates capabilities for storing and managing experimental data from X-ray crystallographic and mass spectrometry experiments with modelling and simulation tools and enterprise data management.

“Merging functionality from both our QUANTA and Insight II products through DS Modeling marks a major step towards delivering a complete discovery solution that’s easily accessible to most scientists,” said Dr. Scott Kahn, chief science officer at Accelrys. “DS Modeling’s comprehensive informatics environment incorporates valuable prior knowledge, giving scientists access to better, more complete information to help focus the search for potential protein targets for drug discovery.”

The DS Modeling components being released today include the following:

DS HT-XPIPE – Complete structure determination of protein-ligand complexes with automated protocols for phasing by molecular replacement, structure refinement, ligand fitting, and solvent placement.

DS XBUILD – Highly interactive module for fitting protein structures into electron density maps incorporates various algorithms for model building, loop fitting, and real-space refinement.

DS XLIGAND – Semi-automated ligand fitting in electron density maps with intuitive tools and applications accessible though the pull-down menus, toolbars, and shortcuts.

DS CNX X-ray – Based on the widely used X-PLOR and CNS, this module provides a flexible, easy-to-use interface to the powerful protocols used for structure refinement, map calculation, water placement and structure validation using experimental X-ray data derived from crystal diffraction.

DS GeneAtlas(TM) – A powerful set of querying and analysis tools for identifying biochemical function from protein sequences, now has a user-friendly, graphical client interface on Windows to run its automated protein annotation pipeline. New experimental wizards guide users through experimental setup.

DS AtlasStore – A proteomic database that incorporates data-mining and visualization of functional annotation data from genomic data now contains connections to many types of experimental information including X-ray data and parameters along with auto-updates of 3D protein structure data from the RCSB Protein Data Bank. Its flexible query interface lets scientists search using chemistry, biology, and experimental information.

DS MSSearch – Brand new functionality that incorporates experimental data as part of the functional analysis of proteomic sequences. DS MSSearch takes the output from mass spectrometry experiments and uses the information for database searching, yielding a much richer annotation for uncovering the function of experimentally identified protein targets.

About Discovery Studio

Discovery Studio is a powerful research environment for the life sciences that delivers a comprehensive suite of informatics, modeling, and simulation solutions. This enterprise-wide family of products is composed of a wide breadth of tools, client-server applications, and databases for handling the specific research problems encountered by scientists working in the discovery process. The Discovery Studio design enables collaboration across scientific disciplines through a centralized project and knowledge management system, connecting the research conducted by biologists and chemists. In addition, Discovery Studio is an open platform built on industry-standard components so that it can leverage existing IT infrastructure and the integration of third-party applications, public domain, and other in-house developed applications. More information on Discovery Studio can be found at http://www.discovery-studio.com

About Accelrys

Accelrys is a leading provider of software for computation, simulation, and the management and mining of scientific data used by biologists, chemists, and materials scientists for product design, drug discovery, and development. Accelrys’ technology and services are designed to meet the needs of today’s leading research organizations. The company has two main centers of excellence, which are located in San Diego, and Cambridge, UK. These centers combine research and development with facilities to support significant collaborative projects. Accelrys Inc. is a subsidiary of Pharmacopeia, Inc. (NASDAQ: PCOP). More information on Accelrys can be found at http://www.accelrys.com.

by Corinne Jones

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