Accelrys Software: DS Modeling 1.1

DS Modeling 1.1 offers basic functionality focused on protein characterization, X-ray analysis, proteomic functional annotation, and homology modeling.

DS Modeling 1.2 - SBD

DS Modeling 1.2 - SBD offers structure-based design, including evaluation of ligand-protein interactions, de novo design, and docking.

DS Modeling, like our other Discovery Studio products, redefines scientific desktop collaboration and computation through better integration, ease-of-use, and knowledge management.

DS Modeling 1.1

DS Modeling Visualizer

Discovery Studio Modeling Visualizer is the visual framework to the DS Modeling client-server environment. It provides tools for sequence and 3D structure characterization, visualization, analysis, and modeling of molecular systems, allintegrated through an easy-to-use environment, giving you seamless flow of information between all DS Modeling products.

DS Analysis

Analyze and visualize molecular dynamics trajectories of proteins and protein-ligand complexes. Animate, graph, and tabulate results.

DS Biopolymer

For building and modifying peptides as well as splitting, cleaning, editing, mutating and capping/uncapping proteins.

DS CHARMm , DS CHARMm Lite

Calculates energy minimization and molecular dynamics simulations.

DS CNX

Built upon the widely used programs X-PLOR and CNS, DS CNX provides a flexible easy-to-use system that incorporates leading structure solution algorithms to perform macromolecular structure determination.

DS DelPhi

Perform electrostatics and solvation calculations.

DS HT-XPIPE

Automated highthroughput crystal structure determination of protein-ligand complexes. Consists of protocols for molecular replacement, structure refinement, electron density map calculation, ligand fitting and water placement.

DS MODELER

Perform automated protein homology modeling, loop modeling, sequence and structure-based alignments, or build protein mutants.

DS MSSearch

Brings together mass spectroscopy with proteomics, protein modeling, 3D protein annotation, and chemistry lead discovery, allowing mass spec searching of a highly annotated protein database.

DS Protein Families

Calculate multiple sequence alignments using sequence & structure information, and perform. Evolutionary Trace analysis to identify functionally important residues.

DS Protein Health

Determine the quality of protein structures using the Profiles 3D verification method and perform secondary structure classification.

DS Protein Similarity Search

Identify homologs for your protein sequences by searching over the web or against locally installed databases.

DS XBUILD

Protein model building and refinement tools in an intuitive and semi-automated environment.

DS XLIGAND

Powerful drug discovery tool that semi-automatically fits ligand molecules to electron density maps of protein-ligand complexes.

DS Modeling 1.2 - SBD

DS Modeling Visualizer

DS Modeling Visualizer for DS Modeling 1.2 - SBD is an advanced visual framework that provides integrated 3D molecule views, ligand tables, and hierarchical views of your data. A tool for calculating ligand RMSDs using topological symmetry is also provided.

CFF

CFF (Consistent Force Field) is a forcefield applicable to proteins, other macromolecules and small drug-like molecules. CFF can be used with DS LigandFit, DS LigandScore, and DS CHARMm Lite.

DS CHARMm Lite

DS CHARMm Lite is used for in situ ligand minimization using the CHARMm simulation engine. DS CHARMm Lite is functionally equivalent to C2.Minimizer and the minimization capabilities of Discover, however it does not include the ability to perform molecular dynamics or Monte Carlo simulations.

DS LigandFit

DS LigandFit provides docking capabilities previously only available in C2.LigandFit. Additional functionality includes full parallelization on all platforms and an option to concatenate experiments automatically with in situ ligand minimization using DS CHARMm Lite and scoring using DS LigandScore.

DS LigandScore

DS LigandScore enables the user to objectively evaluate ligand-protein interactions with scoring functions and their individual descriptors. The scoring functions include LigScore2, PLP1, PLP2, Jain, PMF, and Ludi energy estimates. Also, a Consensus Score can be calculated from scoring results to rank ligands in virtual screening studies.

DS Ludi

This is Accelrys' de novo design engine from Insight II and Cerius2. DS Ludi can be used for Receptor-based de novo searching of fragments ('Receptor' mode) and for building on an existing ligand scaffold ('Link' mode). Ludi score functionality is also available in DS LigandScore to Ludi users.

LigandFit/CAP

LigandFit/CAP is a library of ligands in 3D representation prepared from the Chemicals. Available for Purchase (CAP) and CAPScreening databases. All ligands in the LigandFit/CAP database are commercially available.

Ludi/CAP

Ludi/CAP is a fragment library derived from the CAP (Chemicals Available for Purchase) database designed specifically for Ludi. This library can be used for Receptor-mode de novo design using the Ludi engine and can be accessed by the Ludi engine in any of the three interfaces, DS Modeling 1.2 - SBD, Insight II, or Cerius2.