Drug Design - Fast and Efficient Generation of 3D Molecular Models


The rule and databased computer program CORINA (COoRdINAtes) automatically generates three-dimensional atomic coordinates from the constitution of a molecule as expressed by a connection table or linear string, powerful and reliable to convert large databases of several hundreds of thousand or even millions of compounds.

CORINA is applicable to the entire range of organic chemistry. All structures which can be expressed in a valence bond notation can be processed, including stable molecules, radicals, reactive intermediates, multi-fragment records (e.g. salts), fused rings, spiro, polycyclic and polymacrocyclic systems. Stereochemical information is also considered and atoms with up to six neighbors are allowed. Thus, even metal complexes can be processed.

There are no upper limits to the size of the molecule or to size of rings. By default, CORINA generates one low-energy conformation for each input structure. For rings consisting of less than ten ring atoms, multiple conformations can be generated - a useful feature for generating flexible 3D databases.

The input structures can be processed in a variety of file formats (e.g. MDL SDFile and RDFile, SMILES, SYBYL MOLFILE and MOL2 format, or CTX). Different output file types can be chosen (e.g. MDL SDFile and RDFile, SYBYL MOLFILE and MOL2 format, PDB, or CTX).

CORINA delivers structures of high quality. The RMS deviation of CORINA built models from published X-ray structures is among the best of all commercially available conversion programs.

CORINA is fast (less than 1 sec for small and medium organic molecules), robust and provides excellent conversion rates (99.5%) for the 250,251 structures of the National Cancer Institute (NCI) Open Database without intervention or program crash.

CORINA is general. The Beilstein database with more than six million compounds has been converted with conversion rate of more than 99%.

CORINA has been made accessible to the scientific community via our Free On-line Service.

More information about CORINA is available from Molecular Networks GmbH.


Sadowski, J.; Gasteiger, J.
From Atoms and Bonds to Three-dimensional Atomic Coordinates: Automatic Model Builders.
Chem. Reviews, 1993, 93, 2567-2581.

Sadowski, J.; Gasteiger, J.; Klebe, G.
Comparison of Automatic Three-dimensional Model Builders Using 639 X-Ray Structures.
J. Chem. Inf. Comput. Sci., 1994, 34, 1000-1008.

Schoenberger, H.; Schwab, C.H.; Hirsch, A.; Gasteiger, J.
Molecular Modeling of Fullerene Dendrimers.
J. Mol. Model., 2000, 6,379-395.


Dr. Christof H. Schwab
CORINA is commercially available at Molecular Networks GmbH.
For further information please send a message to info@molecular-networks.com.