software for cheminformatics

Applications: Lead discovery and optimization.

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A fast and powerful 3D structure generator for small and medium-sized, typically drug-like molecules. The perfect application to convert large chemical datasets and databases.

CORINA classic
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A cheminformatics application to manage, manipulate and profile molecular data sets for in silico discovery and optimization experiments.

CORINA Symphony

Features & Functionality
 

  • Generates a single, high-quality and low-energy conformation (default)

    • Optionally generates multiple conformations for ring systems (up to 9 ring atoms)

  • Properly processes stereochemical information

    • Tetrahedral centers, cis/trans double bonds and atropisomerism (if coded in input structure)

    • Optionally generates stereoisomers 

    • Handles and optionally enumerates SD V3000 stereochemical representations

  • Includes optional structure clean-up and standardization features

    • Canonicalizes structures internally to ensure atom numbering-independent conformations

    • Removes small fragments in records, such as solvents or counterions

    • Neutralizes formal charges

    • Adds implicit hydrogen atoms

    • Re-assignement of atom types

    • Orientation according to moments of inertia

  • Handles a broad range of organic chemistry and even organometallic compounds with atoms with a coordination number of up to 6

  • Reproduces experimentally determined X-ray structures and generates close-contact free conformations shown on a dataset of over 21,000 X-ray structures

    • About 35% of the generated 3D models have an RMS deviation of ≤ 0.5 Å to X-ray geometries

    • More than 98% of the generated 3D models have a close contact ratio of ≥ 0.8

  • Processes the NCI Open Database (version May 2012) with 265,242 small to medium-sized molecules in approximately 10 minutes on a 64 bit Linux workstation with a conversion rate of 99.6%

CORINA Symphony combines the unique features of CORINA Classic for structure standardization, clean-up and 3D model generation with powerful and fast methods for structure representation and descriptor and property calculation including the effective chemotype profiling approach known from the ChemoTyper application.

Furthermore, CORINA Symphony provides means to store, manage and manipulate chemical data sets along with chemical, biological or physicochemical properties in a robust and efficient database backend.

Features & Functionality
 

  • Applicable to a broad range of chemical compound classes

  • Workflow-based and interactive processing of chemical data sets

    • CORINA Clean/3D workflow for structure clean-up and standardization and 3D generation

    • CORINA Descriptors workflow for calculation of descriptors, properties and chemotypes profiles

  • Fast and reliable conversion of molecules into uniform descriptors encoding structural and physicochemical features and fingerprints

    • Provides global molecular, shape and size-related descriptors, surface-based properties and EMPIRE quantum-mechanical parameters NEW (optional)

    • Houses the ToxPrint chemotypes library containing over 700 chemotypes for profiling, grouping and categorizing chemical compounds

  • Database backend to efficiently store and manage chemical and associated data

  • Table view for data set inspection and manipulation with editable table cells and copy&paste functionality into external spreadsheet applications

  • Support of standard chemical (e.g., SD or SMILES) and table file formats (e.g., TSV or CSV) for import and export

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