Accelrys Software: INSIGHT II
Insight II® is a sophisticated molecular modeling environment, integrating a powerful molecular graphics interface with tools and applications for biomolecular engineering, modeling and simulations. Insight II combines industry leading codes for applications including homology modeling, simulations, de novo ligand design, and electrostatics with interactive graphs and tables, enabling researchers to get quality results rapidly.Insight II currently runs on Intel-compatible workstations running Red Hat Enterprise Linux and SGI workstations running IRIX®. Some computational servers are also support on IBM AIX®.
For PC-based life science modeling, see DS ViewerPro and DS Modeling. For PC-based materials modeling, see Materials Studio.
Insight II provides the core environment for all Insight II software modules, and the ability to build, modify, manipulate, display, and analyze molecular systems and related data.
Affinity provides automated docking of ligands to receptors in the structure-based drug design process. These calculations include an implicit solvation term, and the component effects of this term, and of other energetic partitions, can be viewed graphically.
Binding Site Analysis combines several tools that enable you to identify and characterize a protein's binding site, then use those characteristics to look for similar features in other proteins of known structure.
Biopolymer constructs models of peptides, proteins, carbohydrates, and nucleic acids for visualizing complex macromolecular structures and for use in further simulation work.
CFF
An advanced Class II force field, is used to optimize DNA, RNA, carbohydrates, lipids, proteins, peptides, and small-molecule models, giving a high confidence level for calculations in drug discovery, protein design, genomic theraputics, NMR spectroscopy, and X-ray crystallography.CHARMm
A highly regarded and widely used simulation package. CHARMm combines standard minimization and dynamics capabilities with expert features including free energy perturbation (FEP), correlation analysis and combined quantum and molecular mechanics (QM/MM) methods. Simulations provide insight into molecular-level structure, interactions, and energetics.CHARMm/MMFF MMFF from CHARMm
Converter builds 3D models from 2D structural database output.DeCipher
A powerful and flexible program for high-level analysis of molecular structure and the results of molecular dynamics simulations.DelPhi
Calculates electrostatic potentials and solvation energies of both large and small molecules, including nucleic acids. You can use DelPhi to rigorously examine the effects of charge distribution, ionic strength, and dielectric constant on the electrostatic potentials of macromolecules.Discover
A simulation program available within Insight II. It incorporates a range of well validated forcefields for dynamics simulations, minimization, and conformational searches, allowing you to predict the structure, energetics and properties of organic, inorganic, organometallic, and biological systems. Discover also implements IPC (Inter Process Communications), which allows users to instruct Discover to turn processing control over to external programs, and retrieve the results of those external processes, incorporating them into the continuing Discover computations.Homology
Builds a 3D model of a protein from its amino acid sequence and the known structure of related proteins. Standard techniques of backbone building, loop modeling, structural overlay and statistical analysis of the resulting models are available.Insight II creates, modifies, manipulates, displays, and analyzes molecular systems and related data and provides the core requirements for all Insight II software modules.
Ludi
A powerful tool for de novo rational drug design. Ludi can be used to fit molecules into the active site of a receptor by identifying and matching complementary polar and hydrophobic groups.Ludi/CAP
Enables the design tools of Ludi to select commercially-available chemical fragments based on Accelrys's Chemicals Available for Purchase (CAP) and CAPScreening databases. Ludi/CAP provides access to over 65,000 commercially available structures to accelerate your search for drug candidates.MCSS
Characterizes an active site's ability to bind given ligand probes using energetics calculated via CHARMm. This information provides a map of potential binding locations within an active site region for functional groups on ligands that can be used in further drug design studies. Other modules include MCSS/HookMODELER
Quickly and automatically generates a refined homology model of a protein, given only the sequence alignment to a known 3D protein structure. You are able to generate excellent structural models given as little as 30% homology to known structures.NMR Refine Advanced
Expands the refinement capabilities found in NMR Refine/DG-II to include simulated annealing and restrained molecular mechanics and dynamics (MD Schedule), refinement of NOE intensities using hybrid-matrix approaches (IRMA), direct refinement of NOE volumes (NOE-MD), an interface to back-calculating 2D NOESY crosspeak intensities (NOE Simulate), and a spreadsheet method of analyzing NMR-related structural and dynamical molecular parameters (Query).NMR Refine DGII
Provides an entry-level option into NMR refinement software with capabilities for generating structures from NMR-derived distance and dihedral restraints. The DG-II, Restraint Analysis, NMR Database and ProStat pulldowns combine to give the NMR spectroscopist the necessary tools for generating, analyzing and verifying high resolution structures.NMR X-PLOR
Rounds off Accelrys' product offerings for refinement of three-dimensional structures derived from experimental NMR data, by linking the graphical power of Insight II with the powerful structure determination protocols of X-PLOR/DG.Profiles-3D
A patented technology exclusively licensed to Accelrys, uses "environmental classification" of protein residues to assess whether a primary sequence is compatible with the current 3D structural model. Profiles-3D is used to search a structural-motif database with a new sequence, looking for compatibility; search a sequence database with an example stucture, seeking similarity; or verify the agreement between the sequence and current model of a protein sequence/structure under study.Search/Compare
Generates and compares the conformations of different molecules. You can operate on molecular fields and volumes, superimpose two or more molecules, and search systematically for sterically allowed conformations.SeqFold
Provides a new algorithm to aid the functional identification of proteins. Using an approach based on fold recognition, SeqFold helps you to identify homologous proteins when traditional searching methods fail.Sketcher
Used to draw molecules in 2D and automatically convert them to 3D models.Protein modeling and Protein Health
Structure modeling and Validation
QUANTA
An extensive library of crystallographic software programs that streamline and accelerate protein structure solution. What previously required weeks or months to accomplish is now achievable in only hours or days.X-POWERFIT
A unique tool for automatically determining the secondary structure of a protein from MAD, MIR, or SIR electron density maps. This new software can speed up electron density fitting up to 500-fold over conventional methods.X-AUTOFIT
Provides semi-automated tools for de novo carbon alpha tracing into electron density maps.X-BUILD
Designed for model building of molecular coordinates into electron density and is closely linked with X-AUTOFIT. Semi-automated tools help you to significantly speed up the process of fitting your electron density map.X-LIGAND
A powerful tool for drug discovery that automatically fits ligand molecules into electron density of protein-ligand complexes. Thousands of possible conformations can be sampled within seconds.MS Modeling
Materials Studio's modeling and simulation product suite, and is designed for structural and computational researchers in chemicals and materials R&D who need to perform expert-level modeling and simulations tasks in an easy to learn yet powerful environment. It provides flexible and validated tools for the study of materials at various length and time scales.Modeling and simulation allows researchers to screen a wide variety of materials and process variables in silico, fail early, and focus on the most promising candidates for further experimental work. Such methods enable substantial time and cost savings.
