Accelrys discovery studio 2.5

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

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

§ Improvedsupport for handling small molecule data sets.

§ Improvedintegration with Pipeline Pilot.

§ Usabilityimprovements to the Discovery Studio Client.

§ Enhancedconfiguration of the Discovery Studio Client user interface.

§ Newscientific functionality in the following areas: Fragment based design; X-Raystructure determination; small molecule conformational analysis; transmembraneprotein modeling; forcefield analysis; pharmacophore analysis.

Functionalityin these different areas will be covered and demonstrations of key new featureswill be provided.

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

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

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

It isfrequently difficult to experimentally determine the structures of multi-domainproteins and large protein complexes. This webinar will discuss the use ofavailable Accelrys computational tools for protein domain and protein-proteindocking to develop structural models for complete multi-domain proteinstructures and protein complexes.  Examples will be presented illustratingthe use of Mass spectrometric chemical modification and cross linking studiesas constraints in protein domain and protein-protein docking.  Otherexamples presented will illustrate the use of data from mutational studies asconstraints 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

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

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

Pharmacophoreshave been generated for the nuclear hormone receptors such as the Pregnane XReceptor (PXR), which have been then used for predicting potentiallyundesirable drug-drug interactions of antibiotics and other classes ofmolecules of pharmaceutical interest. Computational models of PXR agonists andantagonists have also been used to discover an antagonist binding site,discover new drug-like antagonists and understand the evolution of PXR. We havefound that in contrast to other nuclear hormone receptors, PXRs showsignificant differences in ligand specificity across species. By pharmacophoreanalysis, certain PXRs share similar features such as human, mouse, and ratPXRs, suggesting overlap of function and perhaps common evolutionary forces. The implications and relevance of models for PXR and other nuclearhormone receptors extend from pharmaceutical research to understanding theenvironmental implications of chemicals.

E-Novo Automated Workflow for Structure-Based LeadOptimization
Brad Pearce, Principal Scientist - Computer-Assisted Drug Design, Bristol-MyersSquibb,

Acomputationally efficient automated workflow was developed in Discovery Studiofor structure-based lead optimization. Using 3D coordinates of a protein-dockedligand scaffold, docking efficiency is realized within a congeneric library forvirtual screening. A modified core-constrained CDOCKER protocol usingCHARMm-based tools is a key component along with implicit solvation modelsusing MM-GBSA for scoring the top ranking CDOCKER poses. Protocol validation isprovided with several diverse examples

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

It istoxicology's job to discover a compound’s harmful effects and suggest ways toprevent or mitigate those harmful effects. As toxicity experiments arefrequently very expensive and time consuming, in-silico predictive toxicologytechniques such as TOPKAT provide a fast and cost-efficient alternative and/orsupplement for the identification of toxic effects at an early stage of productdevelopment. This webinar will present the new updated TOPKAT models, and showhow these can be used by chemists, biochemists and biologists from anyorganisation who want to compute and validate assessments of the toxic andenvironmental effects of chemicals solely from their molecular structure.

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

Whetheryou have professional training in macromolecular X-ray crystallography or havea modeling background and want to visualize electron density maps, the newX-ray component collection provides you with a suite of components andprotocols used in the X-ray refinement process. The new collection makes use ofan improved automated typing engine, provides pre-built protocols for refinementjobs including simulated annealing, contains automatic ligand placementcapabilities, as well as various example protocols for automating variousprocesses. If you are a user who is only interested in visualizing electrondensity maps, the new collection reads PDB formatted reflection data, and willquickly generate electron density maps than can be easily displayed in theDiscovery Studio interface. The goal of this webinar will be to provide anoverview of the new X-ray collection, and present a few examples of flexibleworkflows that are now feasible thanks to the integration of X-ray technologyto Pipeline Pilot

Discovery studio 是Accelrys公司的生物信息分析、生物大分子模拟、计算机辅助药物设计软件，该软件采用数据流处理软件Pipeline Pilot作为后台系统，整合了原有insightII, Cerius 2, Catalyst 的功能，可在UNIX、linux、Windows等系统下运行，使用方便，市场占有率较高。

DS中的分子结构显示采用原来的WebViewer，在不断的改进整合中先后改名为DS viewer、DS Visualizer、DSV client，这部分功能是免费提供的。除分子图形显示软件外，Accelrys同时免费提供其分子图形显示插件DSV ActiveX。用户安装该插件后，可以在支持ActiveX的程序中，如Powerpoint、网页甚至自己开发的软件中，以实时交互的方式使用该工具的显示功能，可以大大方便教学和科研工作。

将分子图形嵌入Powerpoint之中有两种方式

1、  为了更方便地创建包含DSV activeX的演示文件，新版本的DSV client可以将分子图形保存为ppt文件，可以打开这个ppt文件，从中拷贝activeX控件到目标Powerpoint中使用即可。

2、  PowerPoint2007，在PowerPoint中打开开发工具选项卡（powerpoint选项>>常用>>在功能区显示“开发工具”选项卡）或者将控件工具添加到快速访问工具栏；
PowerPoint2003，插入控件（具体记不清了）；
在打开的对话框中选择“accelrys DS active control”，然后，鼠标就会转化为一个十字框，按下鼠标，画出一个矩形区域即可插入DSVActiveX对象。此时，对象的内容是空的，没有任何分子。进入显示视图，可以在空间区域右击，选择插入文件，可以打开一个分子图形文件mol2/mol/msv/dsv，然后做出相应修改即可，修改会保存到ActiveX对象中。如果需要保存多种显示模式，可以利用storyboard（右键菜单中可见），非常实用。

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Accelrys discovery studio 2.5