Corina is a computer program developed by the cheminformatics research
group of Prof. Johann Gasteiger at the University of Erlangen, Germany.
Corina automatically generates three-dimensional atomic coordinates
from the constitution of a molecule as expressed by a connection
table or linear code, and which is powerful and reliable to convert
large databases of several hundreds of thousand or even millions of
compounds. Its principal features are:
Corina is applicable to the entire range of organic chemistry.
All structures which can be expressed in a valence bond notation
can be processed.
Stereochemical information is also considered and atoms with up to
six neighbors are allowed. Thus, even metal complexes can be
There are no upper limits to the size of the molecule or to the
size of rings.
- Corina generates by default one low energy
conformation for each input structure. For ring systems consisting
of up to nine atoms, multiple conformations can be generated - a
useful feature for building flexible 3D databases.
The input structures can be processed in a variety of file formats
(e.g. MDL SDFile and RDFile, SYBYL MOLFILE and MOL2, SMILES, 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-sized organic
molecules on a common workstation), robust and provides excellent
conversion rates (99.5%) for the 250,251 structures of the National
Cancer Institute (NCI) Open Database without intervention or
Corina is general. A database with more than six million compounds
has been converted with a conversion rate of more than 99%.
Corina offers many features to influence the 3D generation process,
e.g. addition of lacking or implicitly given hydrogen atoms,
neutralization of formal charges, orientation of the 3D structures
according to their moments of inertia, or removement of counter ions
Corina provides an interface to the flexible ligand docking program
FlexX. During the docking process with FlexX, Corina generates
multiple conformations for the ring systems of the ligand in order
to optimize the steric and electrostatic interactions between the
small molecule ligand and the binding site of the protein.
A superimposition of the experimentally determined structure
of a cyclophane (CSD RefCode: FEFZIZ) and the CORINA built model
(shown in red). The RMSXYZ deviation
of all non-hydrogen atoms is 0.26 Å.
For more information, see the
Corina Home Page at the University of Erlangen
Corina Home Page at Molecular Networks.
Molecular Networks GmbH
Page author: Martin Ott
Last update: Wednesday, 1 September 2004