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Discovery Studio 2.5

Webinar Abstracts

DS Client Overview/What’s new in DS2.5
Paul Flook, Senior Director of Life Science R&D, Accelrys

This presentation will provide a high level overview of Discovery Studio 2.5, the upcoming release of Accelrys computational package for Life Sciences research. The new version of Discovery Studio includes many new features and enhancements which can be grouped according to the following themes:

  • Improved support for handling small molecule data sets.
  • Improved integration with Pipeline Pilot.
  • Usability improvements to the Discovery Studio Client.
  • Enhanced configuration of the Discovery Studio Client user interface.
  • New scientific functionality in the following areas: Fragment based design; X-Ray structure determination; small molecule conformational analysis; transmembrane protein modeling; forcefield analysis; pharmacophore analysis.

Functionality in these different areas will be covered and demonstrations of key new features will be provided.

Fragment-based lead design with Multiple Copy Simultaneous Search (MCSS)
Shikha O'Brien, Director, LS Modeling and Simulations, Accelrys

Fragment-based methods are increasingly becoming popular for lead design and scaffold-hopping in drug discovery. In this webinar we will provide a brief review of all the fragment based design methods in Discovery Studio, and highlight the well-published and validated MCSS methodology. MCSS is a powerful CHARMm-based method for docking and minimizing small ligand fragments within a protein binding site. This scientific functionality can be accessed through a fully automated workflow with associated analysis and visualization tools. With fragment-based docking, accurate scoring and placement of fragments is crucial. We will present recent validation of MCSS using several protein-fragment complexes and show that MCSS is able to recover and identify the X-ray poses.



Protein-Protein Docking and Modeling Protein Complexes with the use of Accelrys tools and Experimental Constraints.
Rachelle Bienstock, National Institute of Environmental Health Sciences

It is frequently difficult to experimentally determine the structures of multi-domain proteins and large protein complexes. This webinar will discuss the use of available Accelrys computational tools for protein domain and protein-protein docking to develop structural models for complete multi-domain protein structures and protein complexes.  Examples will be presented illustrating the use of Mass spectrometric chemical modification and cross linking studies as constraints in protein domain and protein-protein docking.  Other examples presented will illustrate the use of data from mutational studies as constraints in protein docking to obtain structural models
for large protein complexes..



Ligand Design and Drug Resistance in HIV-1 Integrase: Inquiry-based Learning using Molecular Modeling
Eamonn Healy, Professor of Chemistry, St. Edward's University

Here at St. Edward’s we are employing an interdisciplinary methodology for the design of structure-activity probes to elucidate enzymatic activity for a variety of disease states. Molecular modeling, using Discovery Studio and Pipeline Pilot, is used to dock and score varied inhibitors for both wild and mutant forms the enzymatic target.
Utilizing results from our recently completed study of ligand binding in HIV-1 Integrase we have developed a discovery-based learning module for integration into our general education science curriculum. The design and content of this activity, along with an assessment of the pedagogical outcomes, will be addressed in this presentation.



New Uses for PXR Pharmacophores    
Sean Ekins,Collaborations in Chemistry, Jenkintown, PA;
Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD.
University of Medicine and Dentistry of New Jersey - Robert Wood Johnson Medical School, Piscataway, NJ;

Pharmacophores have been generated for the nuclear hormone receptors such as the Pregnane X Receptor (PXR), which have been then used for predicting potentially undesirable drug-drug interactions of antibiotics and other classes of molecules of pharmaceutical interest. Computational models of PXR agonists and antagonists have also been used to discover an antagonist binding site, discover new drug-like antagonists and understand the evolution of PXR. We have found that in contrast to other nuclear hormone receptors, PXRs show significant differences in ligand specificity across species. By pharmacophore analysis, certain PXRs share similar features such as human, mouse, and rat PXRs, suggesting overlap of function and perhaps common evolutionary forces.  The implications and relevance of models for PXR and other nuclear hormone receptors extend from pharmaceutical research to understanding the environmental implications of chemicals.



E-Novo Automated Workflow for Structure-Based Lead Optimization
Brad Pearce, Principal Scientist - Computer-Assisted Drug Design, Bristol-Myers Squibb,

A computationally efficient automated workflow was developed in Discovery Studio for structure-based lead optimization. Using 3D coordinates of a protein-docked ligand scaffold, docking efficiency is realized within a congeneric library for virtual screening. A modified core-constrained CDOCKER protocol using CHARMm-based tools is a key component along with implicit solvation models using MM-GBSA for scoring the top ranking CDOCKER poses. Protocol validation is provided with several diverse examples



Discovery Studio TOPKAT - Chemical Toxicological Assessment
Tien Luu, Lead Scientific Specialist, Accelrys

It is toxicology's job to discover a compound’s harmful effects and suggest ways to prevent or mitigate those harmful effects. As toxicity experiments are frequently very expensive and time consuming, in-silico predictive toxicology techniques such as TOPKAT provide a fast and cost-efficient alternative and/or supplement for the identification of toxic effects at an early stage of product development. This webinar will present the new updated TOPKAT models, and show how these can be used by chemists, biochemists and biologists from any organisation who want to compute and validate assessments of the toxic and environmental effects of chemicals solely from their molecular structure.



Introducing the new X-ray crystallography component collection for Pipeline Pilot and Discovery Studio
Francisco Hernandez-Guzman, Lead Solution Scientist, Accelrys

Whether you have professional training in macromolecular X-ray crystallography or have a modeling background and want to visualize electron density maps, the new X-ray component collection provides you with a suite of components and protocols used in the X-ray refinement process. The new collection makes use of an improved automated typing engine, provides pre-built protocols for refinement jobs including simulated annealing, contains automatic ligand placement capabilities, as well as various example protocols for automating various processes. If you are a user who is only interested in visualizing electron density maps, the new collection reads PDB formatted reflection data, and will quickly generate electron density maps than can be easily displayed in the Discovery Studio interface. The goal of this webinar will be to provide an overview of the new X-ray collection, and present a few examples of flexible workflows that are now feasible thanks to the integration of X-ray technology to Pipeline Pilot

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