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 and its additional structure clean-un and standardization methods make CORINA Classic a perfect application to convert large chemical datasets and 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 most major pharmaceutical and chemical companies and academic research labs 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, 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%

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).