Molecular Modeling and Graphics

The core facility maintains the Discovery Studio molecular modeling package from Accelrys in room C5716, Molecular Visualization Lab.

Discovery Studio Standalone

Discovery Studio Standalone is a complete molecular modeling platform designed for the independent modeler. This standalone environment, powered by the Pipeline Pilot open platform includes the entire infrastructure needed to design and run modeling experiments with Discovery Studio Science. Easily visualize, model, and analyze biological and chemical data using tools for sketching 3D molecules, visualizing dynamic changes, 3D graphing and a host of other functionality. The standalone installation can also be connected into a Pipeline Pilot Server for easy sharing of workflows and data.

Discovery Studio Visualizer Client

Discovery Studio Visualizer Client is a powerful graphical interface to access Discovery Studio Science. DS Visualizer Clients can be inexpensively deployed and easily maintained for research teams while still offering world-class science. When deployed with a Pipeline Pilot Server, DS Visualizer Client offers unparalleled capabilities for sharing data, workflows, and computational resources.

Pipeline Pilot Server

Pipeline Pilot makes the most of your information through industrial-scale data flow control and powerful mining capabilities. You can graphically compose data processing networks, using hundreds of different configurable components for operations such as data retrieval, manipulation, computational filtering, and display. These protocols are automatically captured as you create them and you can even publish them for enterprise-level deployment. Your colleagues have the option to invoke your protocols and run them using their own data using a simple Web interface.

Discovery Studio Free Visualizer

View and share protein and small-molecule data in a clear and consistent way, and in a wide variety of industry-standard formats. This free, easy-to-use visualization tool is an ideal solution for managers and researchers who need to collaborate with modelers, but do not need access to the expert-level analysis tools in Discovery Studio.

DS Analysis

Gain new insights into molecular processes by using DS Analysis to animate, graph, and tabulate results of CHARMm molecular dynamics, small molecule docking, or protein modeling. Analyze MD trajectories in an intuitive, easy-to-use manner by computing the Radius of gyration (RGYR), radial distribution function, clustering of trajectories with ability to select clusters through a dendogram plot, Principle Component Analysis (PCA), and Phi-Psi Time series. Compute RMSD, hydrogen bonds and close contacts for thousands of docked ligand poses in a single job. Calculate RMSD of residues/atoms during the course of a trajectory; display the result in a dendrogram or heat map.

Check the quality of the protein structure and analyze regions with abnormalities using the ‘Protein Health’ toolpanel. Evaluate model quality based on the MODELER DOPE (Discrete Optimized Protein Energy) energy function.