June 2008 eFlash

Accelrys Event:	Accelrys Science and Technology Forums
Webinar Series:	Drug Discovery Webinar Series
Case Study:	Carbon Nanotube Growth Studies at ST Microelectronics
Publication:	Detection of a Formate Surface Intermediate in the Atomic Layer Deposition of High-K Dielectrics Using Ozone
Latest at the Accelrys Community:	New Additions to the Pipeline Pilot Download Library New Modeling and Simulation Protocols in Discovery Studio
Product News:	Announcing the Release of Discovery Studio 2.1 Microsoft SharePoint Integration with SciTegic Enterprise Server
Upcoming Conferences:	CHI Protein Kinase Targets CHI Structure Based Design Conference Listings
Training:	Ongoing Training Opportunities

Accelrys Event

Accelrys Science and Technology Forums - One Week Away
Paris (June 12) • Cambridge (June 26) • Heidelberg (Sept. 18)
The Accelrys Science and Technology Forums 2008 are set to begin next week. The Forums will kick off on June 12 in Paris and will then move to Cambridge, UK on June 26. The Paris and Cambridge agendas are now available online and contain numerous prominent guest speakers from throughout the respective regions. We invite you to join us for these one-day regional events to hear presentations from prominent scientific researchers from industry and academia. You will have the opportunity to learn how innovative computational solutions for modeling and simulation, informatics, and data integration & reporting are being successfully applied to research in the Pharmaceutical/Biotech and Chemicals/Materials industries. Hands-on computer labs with Accelrys scientists will be available for you to get an up-close look at the latest software solutions and find out how they can help address your research challenges. While attendance for all of these events is free-of-charge, we encourage you to reserve your place early as spaces are limited.
See agendas per location and register for an event here >>>

Webinar Series

Drug Discovery Webinar Series - June & July, 2008
Leverage innovative science with an unrivaled ability to easily integrate any third-party algorithm or a relational database, and develop powerful solutions that are ideally tailored to fit your research workflow. Discovery Studio (DS) 2.1, the most advanced computational drug discovery environment available, features significant new science and usability enhancements. Access a novel QM/MM method for refining docked poses and optimizing specialized interaction motifs such as cation-pi interactions. Learn about enhanced capabilities to easily customize DS workflows with an unprecedented level and quality. Join Accelrys scientists for this exciting seven-part webinar series as they present the latest scientific advancements and usability upgrades available to help excel your drug discovery research.
Register and view abstracts >>>

June 12, 2008	Advances in Protein Modeling and Protein-Protein Interactions in Discovery Studio
June 19, 2008	Physics-Based Protein Ionization and pK Estimation
June 26, 2008	Towards Increased Accuracy in Computational Drug Discovery with QM/MM
July 10, 2008	Pharmacophore Guided Fragment-Based Drug Design
July 17, 2008	Advances in Pharmacophore Modeling and Compound Profiling
July 24, 2008	Workflow Customization with DS Developer Client
July 31, 2008	Tips and Tricks in using Discovery Studio

Case Study

Carbon Nanotube Growth Studies at ST Microelectronics
Researchers at ST Microelectronics have used Materials Studio® to study the growth mechanism of carbon nanotubes. The studies revealed that the large free-energy released upon carbon dimer addition to the edge of the nanotube structure is responsible for the extrusive driving force of the growth of carbon nanotubes.
Read the full case study here >>>

Publication

Detection of a Formate Surface Intermediate in the Atomic Layer Deposition of High-K Dielectrics Using Ozone
Jinhee Kwon, Min Dai, Mathew D. Halls, and Yves J. Chabal, Chem. Mater. 2008, 20, 3248–3250

In-situ FTIR studies of O₃ interacting with TMA-derived Al₂O₃ surfaces reveal that O incorporation into the surface results in a stable formate intermediate. DFT calculations provide conclusive band assignments, identifying the surface species. These results have broad implications for understanding the high-κ dielectric ALD process using an O₃ precursor.
Access the full publication (subscription required) >>>

Latest at the Accelrys Community

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. Discussion forums on the website provide an open forum for customers to engage in discussion of scientific and technical topics with one another and with Accelrys scientists. To view details and download the components and scripts, you must first register to become a member.

Want to get automatically updated when new posts are made into the forums? Click here to find out how. Here is the latest:

New Additions to the Pipeline Pilot Download Library

Count Non ring stereocenters in a molecule. Download it here >>>
Schrödinger MacroModel 3D Conformations component. Download it here >>>
Cytoscape Viewer. Download it here >>>
Re-assemble a virtual compound library combinatorially. Download it here >>>

New Modeling and Simulation Protocols in Discovery Studio

Toxicity Prediction (TOPKAT) detailed report. Download it here >>>
Add molecular properties (e.g. IC50, ALogP, etc.) from a CSV file to a multi-conformer database SD file. Download it here >>>
Analyze ligand pharmacophore mapping results by calculating a ROC score.
Download it here >>>
Remove waters from hydrophobic cavities on a protein. Download it here >>>

Product News

Announcing the Release of Discovery Studio 2.1
Accelrys is pleased to announce that Discovery Studio 2.1 is now available for electronic download. This release contains new scientific algorithms, improved functionality, and a large number of usability enhancements.

Notable features include:

DS Developer Client - Easily customize DS protocols/components and integrate third-party algorithms (e.g., proprietary codes, third-party codes, and access to relational databases)
QM/MM - Perform accurate optimization and single-point energy calculations using the combined power of DMol³ and CHARMm. Includes protocols and applications for structure based design and small molecule analysis.
Scripting - Automate routine tasks and develop innovative ways to manipulate and analyze data. Access dozens of scripting examples >>>
Pharmacophores - Access thousands of pharmacophore models in the HypoDB database for compound activity profiling – activity, selectivity, and ADMET. Included are improved capabilities for customizing feature definitions.
Simulations - Calculate per-residue interaction energies and edit force field parameters interactively with updates to several protocols in structure based design. Have full access to the new version of CHARMm34b1.
Protein Modeling - Utilize ZRANK for ranking of protein-protein docked poses generated by ZDOCK. Have full access to the new version of ZDOCK 2.3.

Upcoming Conferences

CHI's Protein Kinase Targets - Boston, June 23-25 - Accelrys, Booth #4

Accelrys will be present at CHI's Protein Kinase Targets, taking place in Boston, June 23-25. Come by the Accelrys booth (space #4) for an up-close demonstration of our latest computational solutions for drug discovery research.
Dipesh Risal of Accelrys will be giving a talk on June 24 at 2:45 PM, entitled, "Tailoring Computational Methods for Kinase Targets". Dr. Risal will highlight Accelrys' suite of programs and tools that are tailored for structure-based design projects involving protein kinases. Several workflows and case studies will be presented that involve not only the docking and scoring against the flexible binding sites of representative kinases, but also tools that allow a visual exploration of the kinome in an intuitive context.
Visit the conference website >>>

CHI's Structure Based Design - Boston, June 25-27 - Accelrys, Booth #7

Join us at CHI's Structure Based Design, taking place in Boston, June 25-27. Stop by the Accelrys booth (space #7) to see our latest computational solutions for structure-based design, including novel methods for structure-based pharmacophores and fragment-based design.
Dr. C.M. (Venkat) Venkatachalam, Accelrys consultant, will be giving a talk on Friday June 27 at 10:45 AM, entitled, "Exploring Receptor-Flexible Docking". Venkat will present a small molecule docking workflow that allows for receptor flexibility using the CHARMm force field. The extent of flexibility in the receptor binding site, as well as the movement of protein side chain atoms in response to a placed ligand, are modeled in this method. Read the full abstract >>>

Conferences Listing
In the coming months, visit us at following events:

NSTI Nanotech 2008 (Boston, MA - June 1-5)
CHI's Protein Kinase Targets (Boston, MA - June 23-25 - Booth #4)
CHI's Structure Based Design (Boston MA - June 25-27 - Booth #7)
Drug Discovery Technology and Development (Boston, MA - August 4-7 - Booth #512)

For the most up-to-date info on our attendance at industry conferences,
Visit the Conferences page >>>

Product Training

Ongoing Training Opportunities
Accelrys offers ongoing training in Life Science, Materials Science, Cheminformatics and Pipeline Pilot.

eFlash Archive