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Discovery Studio Proposal, UGC 01.02.2012

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Discovery Studio Proposal, UGC 01.02.2012 DATASHEET DISCOVERY STUDIO® VISUALIZER 3.0 Molecular visualization is a key aspect of the analysis and communication of molecular modeling studies. It enables a mechanistic understanding of a molecule’s structure to be visualized, so that key insights can be shared between computational modeling experts and collaborating team members. With the release of Discovery Studio 3.0, a single application provides access to both free and fully licensed features. Convert easily from the free to the full version with the addition of a license key. DISCOVERY STUDIO VISUALIZER NEW IN DS VISUALIZER 3.0 With Discovery Studio (DS) Visualizer, the following • 2D Diagram: Create 2D features are available without a license: ligand-receptor interaction • Visualization: diagrams directly in the free Visualizer. – Advanced, flexible molecular visualization tools • New ‘Storyboard’ mode: – Publication quality molecular images Capture key scenes in the – Hardware acceleration and stereo support † Molecule Window and • Ligand-based design: save them to share with colleagues. – Sketching and fragment building tools • Sequence window: – Manual pharmacophore generation Handle and align sequences • Macromolecule design: with multiple chains (e.g., – View and edit molecular sequences Antibodies). In ‘Chain view’, you can swap chain order and align independently. – Superimpose and edit protein structures • ActiveX Control: – Visualize and interact with molecules in Microsoft Office® documents and Internet Explorer † Further information is available at accelrys.com/products/ discovery-studio/requirements/technical-requirements-300.html www.accelrys.com 1 DATASHEET: DISCOVERY STUDIO MOLECULAR VISUALIZATION 3D GRAPHICS AND PERFORMANCE The Visualizer provides functionality for visualizing, analyzing, The DS Visualizer outputs high quality graphics ready to be used and sharing biological and chemical data. It allows you to view for slideshows, posters, or any other presentation format. molecular data from multiple perspectives by providing the options to view data through 3D structures, sequences, and data tables. • New in 3.0! Improved Graphics Performance: The Visualizer makes use of advanced hardware acceleration to improve handling of very large macromolecule systems. • New in 3.0! Shading and Depth Blur: Generate ambient and • Interact with and rapidly analyze your data using the Molecule direct shadows, depth blur, atom contouring and custom Window, which supports visualization, data table and hierarchy backgrounds. views of the data. • Control lighting, depth cueing and graphics quality to enhance • View and manipulate publication quality 3D molecular visualization. structures ranging from atomic-level to large macromolecular complexes. • Generate a variety of charts such as 3D point plots, heat maps and Ramachandran plots to analyze your data. • Scroll through sets of molecules with the help of navigation keys, easily managing complex libraries. • Manage large data sets with ease using the integrated browser in the Molecule window. Visualize structures in different colors by property of interest. • Augment 3D structure appearance with multisided surfaces • Study proteins and nucleic acids using the Sequence Window, and isosurfaces and apply material appearances (e.g., metallic enabling the viewing and comparison of the sequences, or plastic) to create graphics that are polished, professional and alignments and annotations. ready for presentation. • Export jpg, .jpeg, .bmp and .png files. Supported Graphics Cards† • Save high quality 3D graphics as POV-Ray files. The following cards are supported with DS3.0. Where applicable, hardware acceleration and hardware stereo [St] is supported: • ATI FireGL V3600, V5600, V7600[St], V7700[St], V8600[St] Supported Operating Systems† • ATI FirePro V3700, V5700, V8700[St] • Windows and Linux compatible: • NVidia Quadro FX 570, 580, 1800, 3800[St], 4600[St], 4700[St], 4800[St], • Windows: XP, Vista (32bit), Windows 7 (64 bit) 5600[St], 5800[St] • Linux: Red Hat 4 (32/64 bit), Red Hat 5 (64 bit) and SUSE 10 (64 bit) www.accelrys.com 2 DATASHEET: DISCOVERY STUDIO USER FRIENDLY • Calculate solvent accessibility, RMSD and predict secondary structures within a single environment. • Enhanced client usability: Access to DS science (tools and protocols) has been reorganized to reflect the most common workflows. The result is a major improvement in CUSTOMIZATION the accessibility and ‘discoverability’ of science available in DS Visualizer can be customized to suit your workflow: Discovery Studio 3.0. • Add toolbars and buttons, shortcut keys and modify default • Accelrys .dsv file: Save your molecules exactly as seen, parameter settings. including display styles, surfaces, text labels and Sequence • Use autohide to hide dockable windows and maximize the Windows in the updated .dsv file format. workspace for visualization. • Undock tabbed windows and manage them outside the main application window. • Simplify workflows by dragging and dropping files from your desktop or file explorer. • Use Perl scripting to automate molecular manipulation workflows. ActiveX Control * IMPORT, BUILD AND ANALYZE STRUCTURES DS Visualizer ActiveX Control is an integratable viewer that provides interactive 3D visualization of small molecules, proteins, nucleic acids, DS Visualizer handles the transfer and analysis of a variety of crystal structures and pharmacophore models. data types including 2D and 3D structures, sequences and • Insert interactive molecular graphics into a Microsoft PowerPoint graphics. You can download structures and sequences directly presentation to create powerful presentations with the ability to from the PDB, or NCBI. You can also edit structures and perform manipulate (rotate and zoom) and analyze data. calculations to gain further insight into their molecular properties: • Add custom buttons or right-click options to modify the chemistry and display of the data during a presentation. • Sketch, build and modify 3D structures using sketching and • Enhance web pages with dynamic 3D molecular visualization. fragment building tools. • Superimpose structures based on tethers, residues or sequence alignment. • Manually derive pharmacophore models from small molecules or protein-ligand complexes. • Visualize properties of large sets of molecules with a user- defined color scheme. • View molecular data in multiple perspectives such as 3D structure, sequence, chart/graph and data table. • Alter geometric and chemical properties and monitor structural orientations and interactions within an interactive environment. * DS Visualizer ActiveX Control is an independent product and is available as a separate free download with DS Visualizer. It does not require the installation of DS Visualizer www.accelrys.com 3 DATASHEET: DISCOVERY STUDIO DISCOVERY STUDIO 3.0 VISUALIZER: • Licensed: With the addition of a client license, all available FREE VERSUS LICENSED MODE features are exposed in the client interface, without need to upgrade or reinstall: • Free: In ‘free mode’, a limited set of functions are available, allowing you to view and edit data files created with Discovery – Connect to Pipeline Pilot™, enabling access to licensed Studio and other applications. You can view and edit scientific functionality including, macromolecule design, molecular structures, sequences, sequence alignments and ligand-based design, virtual screening, ADMET prediction Perl scripts. Additionally, a subset of the Discovery Studio Perl and more. † API is available. – View and customize protocols, share them with colleagues, and run them from the Discovery Studio or Pipeline Pilot client. † Type Feature Free Licensed Supported on Windows 7, Vista, XP and Red Hat Linux 4.0, 5.0, and SUSE 10 New! Welcome Page with quick access to files and information Custom short-cut keys and toolbars Client Perl scripting Files explorer view Table browser for small molecule data sets Protocols, jobs, parameter help, and tools explorer views Unified Molecule Window with 3D view and associated hierarchy and data table views Create multiple sided surfaces and isosurfaces for enhanced molecular visualization Access to charts, including 2D (line and point), 3D point plots, heat maps, histograms and more New! Force field typing for generation of parameter and topology files used in molecular simulationsNew! Constraints and restraints setup for molecular simulations New! Molecular Dynamics Simulations † General Superimpose structures based on tethers, residues, sequence alignment New! Superimpose structures based on molecular overlay functionality RMS calculations Transformation matrix and center of geometry Calculate basic molecular properties New! Launch protocols from the toolbar † Molecular Builders for peptides and nucleic acids New! Access to Side-Chain Rotamer conformations and interaction analysis New! Structure superimposition by alignment New! Structure and Sequence alignment † Support for a variety of sequence-structure formats Sequence windows Secondary structure prediction Protein Graphing functionality, including Ramachandran and contact plots New! Contour and display X-ray electron density maps 3D pointer to navigate structures and place 3D labels New! Basic tools to edit X-ray structures New! Build and refine X-ray Structure Place and refine X-ray Ligand Structure Dendrogram toolbar Access protocols to prepare, minimize and refine protein structures, generate protein reports and validate protein structures † View two-dimensional
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