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June 2007 eFlash
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Application Notes
Antibody Modeling: A Quick Reference Guide to Building Antibody Homology Models and Graphical Identification and Refinement of CDR loops in Discovery Studio
This application note presents a quick reference guide for constructing antibody homology models using MODELER in Discovery Studio®. Models are then screened for quality and further refined with tools in Discovery Studio. Additional analysis tools are also introduced to further help in the structure refinement and quality improvement of the newly built model.
Download Application Note >>>
Automated De Novo Design Workflow with Physics-Based Scoring Function for Fast Lead Identification and Optimization
This application note discusses the preparation of a protocol created in Pipeline Pilot with existing Discovery Studio 1.7 components that automates the generation of new ligand molecules created by fusing suggested fragments to a scaffold, followed by further refinement and physics-based scoring (MM-GBSA) using CHARMm for ranking. Download Application Note >>>
Publication
Structure of Phase III of Solid Hydrogen
Recent work with CASTEP illustrates how Density Functional Theory (DFT) can be used to predict phase diagrams of materials. Appearing in Nature Materials, work by Chris Pickard at the University of St Andrews and Richard Needs of the Cavendish Laboratory led to a radical revision of the phase diagram of hydrogen up to nearly 400 GPa. One of the new predicted phases is calculated to be stable over a wide range of pressures, and its vibrational properties agree with available experimental data.
Read More >>>
Webinar Series
Accelerating Discovery and Development Research - Scientific Data Integration and Dashboards
Improve your scientific and corporate decision making by discovering how you can create dynamic data flows and applications that allow you and your colleagues to use Pipeline Pilot to integrate, analyze and view diverse data types and sources. This webinar series, which features guest presentations from our software partners, will show you how to integrate chemistry, sequence, image, and text data to build powerful analytical environments. You'll find out more about dashboards that present integrated, high-level data, while allowing you to drill-down to reveal detailed information. You will see examples ranging from scientific applications for refining experimental designs, hypotheses and data interpretation, to business analytics applications—all of which are designed to enable you to efficiently drive your scientific and corporate strategy.
Join us to learn more in the following areas:
- May 23, 2007: Using visual programming to capture best practices in discovery and development research (Recording Now Available)
- June 6, 2007: Solving the information overload problem - Integrating disparate data sources and applications
- June 13, 2007: Effective presentation of research results - Reporting and dashboards
- June 21, 2007: Empowering the discovery and development researcher - Deployment of workflows through web portals
Latest at the Accelrys Community
New Materials Studio and Discovery Studio Scripts
The Accelrys Community website provides the opportunity for users to share and download scripts and Pipeline Pilot components written by both users and Accelrys scientists. To view details and download the components and scripts, you must first register to become a member.
Here is the latest:
- A script to perform rigid body optimization on a Polymorph-generated trajectory with new motion groups. Download it Here >>>
- A script to analyze the hydrogen bonds in multiple structures in a study table. Download it Here >>>
- A script for changing the display to highlight protein-ligand hydrogen bond interactions.
Download it Here >>>
Product News
SPRESI for Accord Database Explorer Released
SPRESI is a comprehensive chemical structure and reaction database, providing direct access to millions of chemical structure and reaction entries extracted from a variety of references and patents. You can use SPRESI as a reference source for looking up information on how to make specific molecules for a particular project, saving you the time and trouble of having to look up synthesis information directly in the primary literature.
More Information >>>
Chemicals Available for Purchase (CAP) Release 2007.1 Now Available
CAP is a consolidated database that combines the contents of many vendor catalogs into a single, easy to search relational database. Updated quarterly, CAP makes it easy for you to locate readily available supplies of reagents and compounds from a wide variety of suppliers. Ideal for use by scientists engaged in activities such as chemical synthesis and screening, CAP 2007.1 now covers data from 119 suppliers' catalogs, 7 new to this release.
More Information >>>
Accord Chemistry Control and Accord Grid Control 6.2 Just Released
The Accord Chemistry Control and Accord Grid Control are rapid application development tools that you can use to chemistry-enable Microsoft(R) Windows-based applications. The Accord Chemistry Control enables you to render and manipulate chemistry in your own custom solutions; the Accord Grid Control provides you with the ability to display chemistry and associated data in a tabular or spreadsheet-like format. The 6.2 releases of both products include support for Windows Vista, support for Accelrys' upcoming chemistry drawing editor, Accord Draw and more. Find out more about the Accord Chemistry Control 6.2 >>> and Accord Grid Control 6.2 >>>
Accord Chemistry Java Object (ACJO) 1.2 Now Available
The ACJO is a development component that gives you the ability to chemistry-enable applications built and written in Java, by providing you with a convenient building block that encapsulates commonly required chemistry display and manipulation functionality. This latest version of the ACJO provides faster chemistry rendering, support for Windows Vista and support for Accelrys' soon-to-be released chemistry editor, Accord Draw. Also new in version 1.2 is support for Java Web Start to enable you to produce single-click, easy-to-deploy applications for end-users. More Information >>>
Accord Draw - Coming Soon!
Accord Draw is a new desktop chemistry editor that you can use to draw chemical structures and reactions for use in registration, searching and chemistry data submission to a variety of applications, such as corporate registration systems, inventory systems and electronic laboratory notebooks. Accord Draw 1.0 is due for release in late summer. Click here for a sneak peak and to sign up for product updates and more information >>>
Upcoming Conferences
CHI Structure-Based Drug Design - June 6-8, 2007 - Boston, MA
Join us during the Technology Watch session and listen as Dr. Dipesh Risal of Accelrys discusses a new flexible docking solution in the integrated software environment, Discovery Studio. With Pipeline Pilot, this solution can be complemented with fragment-based and pharmacophore-based methods to create customized workflows.
Stop by booth #8 to learn more about our computational drug discovery solutions. While you're there, enter for a chance to win an iPod Nano and pick up your free copy of Discovery Studio Visualizer, which provides a rich set of molecular visualization tools, and includes DS Visualizer ActiveX Control for interactive 3D presentations.
4th Joint Sheffield Cheminformatics Conference -
June 18-20, 2007 - Sheffield, UK
Visit our booth to learn more about the wide range of cheminformatics solutions Accelrys offers. Speak with our specialists to find out how you can get a customized cheminformatics assessment.
7th International Conference on Atomic Layer Deposition -
June 24-27, 2007
Stop by and view our poster at this conference, which will take place at the Kona Kai Resort in San Diego, CA. Dr. Matthew Halls of Accelrys will be presenting a poster entitled, "Computational Tools for Understanding Atomic Layer Deposition (ALD)." In his poster, Dr. Halls will present a summary of the techniques available for studying the structures, mechanism and energetics relevant to semiconductor surface reactions involved in processes such as Atom Layer Deposition (ALD), along with a case study on the reaction of the ZrCl4 precursor with Si(100)-2x1 substrates representative of the early stages of the ALD of ZrO2.
Drug Discovery & Selection - July 4-5, 2007 - Lille, France
Renaud Feix of Accelrys will be presenting a poster entitled, "A Pharmacophore-Based Approach for Activity Profiling for Bio-Active Molecules." Stop by and speak with Renaud to learn more about Accelrys' pharmacological profiling solutions. If you would like to arrange an individual meeting, contact Renaud at rfeix@accelrys.com
Conferences Listings
In the coming month, visit us at the following conferences:
- VI European Workshop in Drug Design (June 3-10; Siena, Italy)
- CHI Structure-Based Drug Discovery (June 6-8; Boston, MA)
- North American Catalysis Society Meeting (June 17-22; Houston, TX)
- 4th Sheffield Conference on Cheminformatics (June 18-20; Sheffield, UK)
For the most up-to-date info on our attendance at industry conferences, visit our website >>>
Product Training
2nd Computational Nanoscience Consortium (CNC) Workshop at NANOTEC (only available to Nanotech Consortium members)
The 2nd Computational Nanoscience Consortium (CNC) Workshop took place at the National Nanotechnology Centre (NANOTEC) in Bangkok on the 16th and 17th of May, 2007. NANOTEC is one of the 28 members of the Nanotech Consortium started by Accelrys in 2004 with the aim to deliver state-of-the-art nanotechnology software tools to enable the Computer Aided Nano-design (CAN) of nanomaterials and nanodevices. The purpose of the two-day workshop was to show the user how to apply the different software tools in real-life research and applications. The training covered the different modules implemented in Materials Studio by Accelrys within the Nanotechnology Consortium: ONETEP, GULP, QMERA and Adsorption Locator. Members of the Nanotech Consortium can access the training material from the 2nd CNC Workshop at NANOTEC. The next workshop for Nanotech Consortium members will be held in Cambridge, UK on June 18, 2007.
Ongoing Training Opportunities
Accelrys offers ongoing training in Life Science , Materials Science , Bioinformatics , Cheminformatics and Pipeline Pilot.
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