CORINA Classic - High-Quality 3D Molecular Models


CORINA Classic (the classic command-line version of CORINA) is a fast and powerful 3D structure generator for small and medium sized, typically drug-like molecules. Its robustness, comprehensiveness, speed and performance makes CORINA Classic a perfect application to convert large chemical datasets or databases.

CORINA Classic matured through a series of versions during the past decades and has become the recognized world-wide gold standard in industry and academia to generate 3D molecular models of high quality. Currently, CORINA Classic is used by BIOVIA, NCI/NIH and most major pharmaceutical and chemical companies to convert their 2D structures into 3D.

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 and cis/trans double bonds (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
  • Handles a broad range of organic chemistry and organometallic compounds with atoms of up to a coordination number of 6
  • Reproduces experimentally determined X-ray structures and generates close-contact free conformations shown on a dataset of over 25,000 X-ray structures
    • Almost 30% of the CORINA-generated models have an RMS deviation of below 0.3 Angstroem compared to the X-ray geometries
    • 98% of the CORINA-generated models have a close contact ratio of greater than 0.8
  • Processes the NCI Open Database (version May 2012) with 265,242 small to medium-sized molecules in approximately 15 minutes on a 64 bit Linux workstation with a conversion rate of 99.6%

User Interface

  • Command line interface supporting batch mode
    • Supports a large variety of chemical file formats such as SD/RD (V2000/V3000), SMILES, InChI, SYBYL MOL/MOL2, MacroModel, Maestro, PDB, CIF and others
  • Component for KNIME analytics platform (on request)

System Requirements

  • Microsoft Windows 7/8/10, Server 2008, Server 2012
  • x86 Linux RHEL5/6

Additional Info

Downloadable PDFs

Slide Show

CORINA - 3D Structure Generation

Online Demonstration

CORINA Classic can be tested free of charge online.


A demo version of CORINA Classic is available for download in our Download Area (after registration).