Accelrys Software: CERIUS2
The leading modeling and simulation environment for SGI IRIX workstations and other servers, Cerius2 provides a wealth of tools for applications ranging from material science modeling to life science modeling and simulations.Cerius2 provides an easy-to-use simulation and modeling environment, offering a broad range of scientific application modules. Select the modules that are relevent to your research to create a customized and integrated package.
C2.AutoLudi builds on the functionality of C2.Ludi Receptor-based de novo design in Link Mode.
C2.Align aligns sets of molecules for easy comparison during the study of drug candidates using automated or manual alignment methods.
3DKeys provides pharmacophore fingerprint capabilities.
# C2.CYP2D6: Predicting cytochrome P450 2D6 enzyme inhibition
# C2.Hepatotoxicity: Predicting compounds with potential liver toxicity
# C2.PBind: Predicting serum protein binding of ligands
C2.Analog Builder is used to specify combinatorial libraries and select fragments/reagents based on their diversity. You can generate sets of congeneric analogs that can be rapidly screened to identify drug candidates.
C2.Conformers provides conformational search algorithms and associated analysis tools, allowing you to characterize molecular conformation and flexibility, and gain insight into geometric and energetic properties.
C2.CSAR uses a recursive partioning methodology to derive decision trees based on qualitative information. The statistical treatment in C2.CSAR is ideally suited for analysis of large data sets from HTS experiments.
C2.DBAccess provides direct access to structural databases (Catalyst and MDL ISIS) for use in modeling experiments. Hits can be browsed in 2D or 3D.
C2.Descriptor+ extends the range of QSAR analysis in Cerius2 by supplying a wide range of generic descriptors. The capabilities of C2.QSAR+ and C2.GA can be applied to problems like combinatorial chemistry analysis, optimization of formulations, and the properties of polymers and blends.
C2.Discover is a user interface to the widely used and well-validated Discover simulation code. Discover provides a broad range of simulation methods, enabling structural characterization and property prediction for molecules, materials, and biological compounds.
C2.Diversity analyzes chemical diversity to design and evaluate compound libraries and reagent sets for combinatorial chemistry. You are able to intelligently sample all potential drug candidates so that a reduced set can be synthesized and screened.
C2.FieldFit performs molecular alignment based on steric and electrostatic fields, as well as alignments on moments of inertia and electrostatic moments.
C2.GA provides the breakthrough technology of Genetic Algorithms to evolve a family of predictive models, which helps you develop QSAR models from receptor surface and other data, leading to faster screening of drug candidates.
C2.Gaussian interfaces to the Gaussian code allowing you to apply ab initio, semi- empirical, and density functional techniques to study the energetics, structure, and chemistry of molecules and transition states.
C2.LibCompare provides multiple library selection and comparison capabilities. It helps keep chemical redundancies to a minimum by providing information such as the overall distribution of compounds in property space, and the incremental diversity resulting from adding specific sets of compounds.
C2.LibEngine provides extremely fast calculations for a number of descriptors; it also provides very fast relocation clustering which can be used for compound selection.
C2.LibProfile provides constrained diversity selection within Cerius2.
C2.LibSelect provides combinatorial library selection capabilities. It incorporates experimental constraints using array design methodologies that are efficiently coupled to the parallel synthesis process, and to the synthesis of combinatorial mixtures.
C2.LibX provides capabilities for subsetting extremely large virtual libraries into realistic size subsets. It also contains library optimization capabilities based on a genetic algorithm.
C2.LigandFit provides accurate and fast flexible docking and scoring capabilities for ligands to a receptor site. Automatic active site finding explores multiple hypotheses for binding site location. Docking can be distributed to AIX, Linux, and SGI servers. Docking and scoring jobs are massively parallelized through United Devices' MetaProcessor Platform.
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.
C2.Ludi is a de novo design program that also allows you to simulate screening before performing experiments and prioritize lead candidates before you synthesize compounds. C2.Ludi also allows you to explore databases of potential ligands or make changes to exiting ligands by scoring candidate structures against the protein active site.
C2.Mechanical Properties predicts a range of ideal elastic modulii for any materials type, helping you to design novel crystalline and amorphous polymers, ceramics, and semiconductors.
C2.MFA permits field-based 3D QSAR and visualization. You can predict the activities of new molecules based on the geometric properties of existing compounds.
C2.Minimizer predicts low-energy structures using molecular mechanics calculations and the power of Cerius2's Open Force Field. C2.Minimizer helps you to gain increased understanding of molecular, macromolecular, amorphous, crystalline, and surface structure and properties.
C2.MMFF provides specialist access to the Merck Molecular Force Field for accurately studying the structure, energetics, and dynamics of molecular systems in the life sciences. MMFF is broadly parameterized for organic and bio-organic systems and for the intermolecular interactions crucial to enzyme binding.
C2.Mopac interfaces to the popular semi-empirical quantum code MOPAC. You can study molecular structure and energetics, and compute properties such as molecular orbitals and charges.C2.NNet uses neural nets for predicting activities or activity classes in SAR analysis or in library focused design.
C2.OFF (Open Force Field) provides molecular mechanics force fields to support Cerius2's property prediction modules. You can choose from an extensive database of force fields covering organics, polymers, zeolites, organometallics, and other materials types.
C2.QSAR+ provides a wide range of regression and analysis technologies integrated in a "chemically aware" molecular spreadsheet. Existing data can be used to predict the activities of novel drug candidates.
C2.Receptor lets you prioritize lead candidates for drug development by investigating their interaction with a protein receptor site - represented as a 3D surface. You can develop predictive QSAR models or rank the results of a database search by volumetric similarity.
C2.SBF provides structure-based focusing capabilities with fast prioritization of databases of compounds against a given target. Fast scoring of compound collections gives direct insight into their complementary features and their potential as lead candidates.
C2.Visualizer provides a comprehensive modeling environment for building, editing and visualizing models of molecular structure as well as the core requirements for running Cerius2 applications. The Protein Active Site Viewer within this module helps you visualize the key elements of protein structure and protein-ligand interactions. A "Hit-List-Browser" is included to review an active site, enabling you to visualize the results of a database search in the context of the protein active site.
C2.X-GEN processes X-ray diffraction data for macromolecular X-ray crystallography. You can take input from multiple detectors and rapidly index and clean up the data - making it suitable for input to refinement packages such as X-PLOR.
C2.Zindo is a powerful semi-empirical QM code that calculates the electronic and structural properties of molecules in gas phase or in solution. Optimized for prediction of UV/visible spectra.
