DS_visualizer_0407.pdf

Windows and Linux-

based visualization,

analysis, and sharing

of biological and

chemical data

Discovery Studio

Discovery Studio Visualizer

Customize the

interface for your

unique needs

Molecular visualization is a key aspect of data analysis that can provide understanding about the implications

of a molecule’s structure on certain interactions and biochemical reactions, while often divulging mechanistic

insight about a biochemical pathway or lead compound. Many sophisticated visualization tools are available

in the Discovery Studio® (DS) Visualizer, which is a Windows- and Linux-based software solution for life science

visualization, modeling and analysis.

Molecular Visualization

•

All of the windows associated with molecular

data, such as the 3D and sequence windows, are

interconnected to allow for interactive selection

for rapid and simpliied analysis of your data.

Include ActiveX control

in presentations for

powerful interactive

3D visualization

The DS Visualizer provides functionality for

visualizing, analyzing and sharing biological and

chemical data. DS Visualizer allows molecular data to

be viewed from multiple perspectives by providing

the options to view data through 3D structures,

sequences, and data tables.

Structure Importing, Building and Analysis

The Discovery Studio Visualizer is a very lexible

environment that allows data to be transferred and

analyzed in multiple formats. Several ile formats for

3D structures, SMILES, sequences and graphics are

supported. Structures and sequences can be accessed

and imported directly from the PDB or NCBI. The DS

Visualizer includes many tools that allow you to edit

your structure and perform calculations to help you

gain further insight into its molecular properties.

•

Your 3D structures can be easily sketched, built, and

modiied with sketching and fragment builder tools.

The interactive environment allows you to alter

geometric and chemical properties, as well as

monitor structural orientations and interactions.

•

DS Visualizer includes tools for calculating

solvent accessibility and RMSD, and predicting

secondary structures.

DS Visualizer can be used to analyze protein sequence alignment

iles, small molecules, protein structures and more.

•

Within the 3D window, you can view and

manipulate high quality 3D molecular

structures ranging from the atom level to large

macromolecular complexes.

•

The hierarchy view in the 3D window provides

easy manipulation, browsing and selection of the

molecules or assemblies.

•

When studying proteins or nucleic acids, the

sequence window provides views of sequences

and sequence alignments for sequence to

structure comparison, sequence annotation, or

sequence family analysis.

Imatinib mesylate (Gleevec) is an enzyme inhibitor used for cancer therapy,

shown mapped to pharmacophore features. Red, Positive ionizable. Green,

HB Acceptor. Magenta, HB Donor. Orange, Ring aromatic.

Discovery Studio

With these tools, acquiring, building and analyzing

molecular structures is convenient, straightforward

and well suited to meet your visualization and

analysis needs.

Organizational Scheme

DS Visualizer conveniently stores, searches and

organizes your iles in a customizable, lexible

‘Explorer’ view. The Files Explorer allows you to

quickly store, retrieve, and manage data, scripts and

experiments saved in your ile system or mounted

drives. In addition, history and sample data can be

quickly accessed.

Customization

The DS Visualizer helps streamline your worklow

by letting you tailor the environment to it your

personal preference and needs.

•

The interface can be customized by adding

user-deined toolbars and buttons, shortcut

keys, and modifying default parameter settings;

your unique customized user interface will then

persist for each session.

ActiveX Control

The DS Visualizer ActiveX Control is a molecular

viewer that provides interactive 3D visualization of

proteins, nucleic acids, pharmacophore models, crystal

structures, and small molecules.

•

You can simplify your worklow by dragging and

dropping iles from your desktop or ile explorer

window directly into DS Visualizer.

•

Insert the ActiveX Control with high-quality

molecular graphics functionality into Microsoft

PowerPoint to create powerful presentations

with the ability to manipulate (rotatable

and zoom) and analyze your molecule. Add

customizable buttons or right-click options that

allow you to modify the chemistry and display of

your molecule during your presentation.

Display and Graphical Output

Once you are ready to present your results, the DS

Visualizer will allow you to change the display style

of molecular and sequence and output high quality

graphics that are ready to be used for slideshows,

posters, or anything else you need.

•

Enhance webpage graphics by adding dynamic

3D molecular visualization in HTML format

through Microsoft Internet Explorer.

•

Build 3D molecular visualization into your

custom desktop applications including scripting

object through Visual Basic and Java.

Interactivity between the 3D Structure and Sequence Windows

guides you to focus on key active sites and ligands.

•

You can control lighting, depth cueing, and

graphics quality to enhance visualization.

•

You have the ability to augment 3D structure

appearances through multi-sided surfaces and

isosurfaces, and apply material appearances (e.g.

metallic or plastic surfaces) to help your graphics look

polished, professional, and ready to be presented.

Discovery Studio

DS Visualizer versus DS Visualizer Pro

Feature

DS Visualizer

DS Visualizer Pro

Supported on Windows 2000, XP and Red Hat Linux WS 3.0, 4.0

Structure window with 3D view and associated hierarchy

and data table views

Sequence windows

Files explorer view

Table browser for MDL sd iles

Secondary structure prediction

RMS calculations

Support for a wide variety of sequence-structure formats

Ability to sketch molecules in 3D and Catalyst pharmacophores

Ability to contour and display X-ray electron density maps

Ability to superimpose structures based on tethers,

residues, sequence alignment, transformation matrix

and center of geometry

Customization of short-cut keys and toolbars

Create multiple sided surfaces and isosurfaces for enhanced

molecular visualization

System Requirements:

ActiveX Control*

DS Visualizer is

supported on Windows

and Red Hat Linux

platforms. For detailed

information, please visit

the Discovery Studio

page on our website,

www.accelrys.com.

Protocols, jobs, parameter help, and tools explorer views

Graphing functionality, including Ramachandran and contact plots

Atom typing for preparing molecules prior to energy calculations

Deine, display and edit binding sites

Modify conformations using a tool panel with the ability to perform

Dreiding minimization, coordinate kick, and torsion kick

Ability to superimpose structures based on molecular

overlay functionality

Calculate molecular properties

Analysis of CHARMm Trajectories in terms of RMSD, close contacts

and hydrogen bonds

Constraint energy terms for CHARMm simulations

Ability to modify or build custom 3D small molecules using

pre-deined fragments through a toolpanel

Ability to edit and analyze pharmacophore models

Dendrogram toolbar to easily convert data into

interactive dendrograms

Perl Scripting capabilities

* DS Visualizer ActiveX Control is an independent product and is available as a separate download

with DS Visualizer. It does not require the installation of DS Visualizer or DS Visualizer Pro.

0607

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