Discovery Studio

Category Cross-Omics>Agent-Based Modeling/Simulation/Tools

Abstract Discovery Studio® (Life Science Modeling and Simulations) is a single unified, graphical interface for advanced drug design and protein modeling research.

Discovery Studio (DS) contains both established gold-standard applications (e.g., Catalyst, MODELER, CHARMm, etc.) with years of proven published results, as well as cutting-edge science to address today’s drug discovery challenges.

Discovery Studio is built on the Pipeline Pilot Enterprise Server™ operating platform (see G6G Abstract Number 20063), (see G6G Abstract Number 20069), and (see G6G Abstract Number 20172), allowing seamless integration of protein modeling, pharmacophore analysis, and structure-based design, as well as third-party applications.

Discovery Studio Platform --

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.

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 be connected to a Pipeline Pilot Server for the sharing of workflows and data.

Discovery Studio Visualizer Client - is an advanced 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 capabilities for sharing data, workflows, and computational resources.

A set of Perl-based scripting commands, and customized scripts, are also available for the automation and customization of common modeling operations that replicate User Interface (UI) actions or act on DS data models.

Pipeline Pilot Server - Pipeline Pilot makes the most of your information through industrial-scale data flow control and advanced 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.

DS Developer Client - This scaled-down version of the Pipeline Pilot client allows you to customize pre-existing Discovery Studio workflows, and also includes the necessary component collections to enable customization. Add or remove available components from existing DS protocols/components. Create a new component and add to an existing DS protocol.

Discovery Studio Free Visualizer - This free 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.

ActiveX Control - The Discovery Studio Visualizer ActiveX Control is a fully integrated, 3D molecular renderer for the Windows environment, and provides an advanced method of sharing scientific results with colleagues via presentations, web pages, etc.

DS Sequence Analysis --

Sequence Analysis allows you to use the popular BLAST and PSI- BLAST algorithms to identify homologs for your protein sequences by searching databases that are either installed locally or available over the internet at NCBI. Results are presented in an interactive report format that facilitates further analysis and manipulation with other Discovery Studio software.

In addition, access tools for performing 'phylogenetic analysis' and 'Evolutionary Trace' analysis that involves creation of a protein family dendrogram using the hierarchical clustering method and mapping of the info onto your 3D structure.

New functionality in the area of 'Antibody Modeling' uses a pre-compiled Complementarity Determining Region (CDR) loop database to automate the process of CDR identification and annotation. A sequence alignment file of the best aligned hits enables automated loop grafting of the CDR regions.

DS Protein Modeling --

DS MODELER - Automatically and rapidly generate a refined homology model of a protein, given only the sequence alignment to a known 3D protein structure, with this industry-standard for fast homology modeling. DS MODELER is the ideal solution for target discovery and for studying the structure and function of proteins across families.

With DS MODELER, you can evaluate model quality, build protein models and mutants with ligands bound, and perform loop modeling based on a DOPE energy function; carry out structure based alignments; create sequence profiles; and perform remote homology modeling searching.

DS Protein Refine - Optimize a loop region of a protein structure using an in-house developed algorithm based on CHARMm. Generate multiple energy optimized variants of the loop region and browse through loop structures and chart results.

In addition, optimize the side-chain of a protein structure using an in- house developed algorithm based on a systematic searching method and CHARMm energy minimization. Both optimization algorithms have No dependency on initial structure (ab initio approach).

DS Protein Families - Gain a better understanding of the mechanism of protein function at the ‘molecular level’ by analyzing the sequence conservation patterns within a family of protein sequences, as well as the position of those conserved residues on the 3D structure.

DS Protein Health - Protein Health uses a method called Profiles-3D Verify to evaluate the 'protein structure' by comparing its structural environments with the preferred environments of amino acids. Misfolded protein segments within a protein structure can be identified by this method, indicating where additional consideration should be given to structural packing. In addition, check the quality of the protein structure and analyze regions with abnormalities using the ‘Protein Health’ tool panel.

DS Protein Docking - Predict protein-protein structure interactions of novel targets rapidly and accurately with DS Protein Docking. Perform rapid rigid body docking with the well-published ZDOCK algorithm, which employs an FFT-based method using a pair-wise shape complementarity function for identifying docked conformations and scores hits based on atomic contact energies.

Increase the accuracy of docked poses using the ZRANK scoring function. Use the RDOCK algorithm, to refine ZDOCK hits based on a CHARMm energy minimization, and score the poses by CHARMm energy and desolvation energy. Narrow the search and identify poses of interest with advanced clustering methods.

DS Simulation --

DS CHARMm Lite - Obtain more accurate scoring and prioritization of ligands based on predicted receptor affinities using DS CHARMm Lite, a customized version of CHARMm with minimization capabilities.

DS CHARMm Lite performs in situ ligand minimization using the well validated CHARMm and CFF force fields and several minimization algorithms. Selected atoms from the receptor can be included in the minimization protocol. DS CHARMm is scalable for high throughput analysis of large numbers of ligands; all jobs can be run in parallel and in background mode.

DS CHARMm - Leverage this industry-standard program to study the energetics and flexibility of molecules -- from small ligands to multi- component physiological complexes. DS CHARMm is regularly updated to include the latest functionality developed by the scientific community.

DS CHARMm is now completely integrated into Accelrys drug discovery applications within Discovery Studio. Sample receptor flexibility, prior to docking, using CHARMm-based side-chain, and loop-sampling and refinement methods.

Use the power of CHARMm to perform accurate small molecule docking by using CDOCKER. Use prior knowledge to guide docking by adding pharmacophore restraints (requires additional products).

CFF Advanced Class II Force field - Optimize DNA, RNA, carbohydrates, lipids, proteins, peptides and small-molecule models, with high confidence based on the accuracy of results. The force field parameters in CFF (Consistent Force field) were developed by computing the properties of 1,768 different molecules spanning 19,432 molecular structures, resulting in a robust and diverse collection of parameters applicable to most biomolecules and small molecules.

Merck Molecular Force Field (MMFF) - Study the energetics and interaction between macromolecules and ligands with the industry- validated force field MMFF94s that has been broadly parameterized for organic and bio-organic systems and for the intermolecular interactions crucial to enzyme binding.

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 dendrogram 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’ tool panel. Evaluate model quality based on the MODELER DOPE (Discrete Optimized Protein Energy) energy function.

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Manufacturer Web Site Discovery Studio

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G6G Abstract Number 20502

G6G Manufacturer Number 100084