Frequently Asked Questions

CORINA is parametrized for the entire periodic table and all molecules that can be expressed in a vald valence bond (VB theory) notation can be processed.

CORINA does not calculate "real" energies such as obtained from FF or QM calculations. Internally, CORINA uses symbolic energy values (that have been derived from FF calculations) only for ring systems.
For ring systems, a full conformational analysis is performed in order to identify a low-energy conformation.
Finally, the ring systems are relaxed in a so-called "pseudo" force field to optimize the ring skeletons, but without calculating "real" energies.

CORINA cannot generate 3D structures for pi complexes. It processes only molecules that can be expressed in a vald valence bond (VB theory) notation.

In general, CORINA does not have any limitations regarding the number of atoms or bonds of an input structure that should be converted into 3D. However, CORINA has been designed to process small to medium sized organic (typically "drug-like") molecules. The larger a molecules gets the more the intra-molecular interactions gain in importance influencing the secondary structure of a molecule. CORINA can model these interactions only to a limited extend and, therefore, is not able to correctly predict 3D structures of polymers and biopolymers such as proteins, enzymes or nucleic acids.

Basically, there are NO limitations concerning the number of atoms or the number of ring atoms in a molecule in CORINA. However, some file formats do not support more than 999 atoms (or bonds), such as the MDL SDFile (V2000).
There is also NO limitation concerning the number of records (i.e., molecules) in an input file. CORINA consectutively process all records in the file and writes out the generated 3D models. Please note that
hardware platforms and operating systems might have some limitations regarding the file size.

CORINA does not need the 2D information (or structure depict) of a molecule but the connection table (CT) information of a molecule. This information is provided in standard file formats for chemical information (such as MDL SDFile or SMILES). CORINA can also generate a 3D structure from an input SDFile if all (2D) coordinates are set to zero (SMILES also does not provide 2D information).
Since the first commercial version of CORINA, it is fully aware of stereochemistry.
CORINA interprets stereo descriptors in SMILES (@ and @@ for tetrahedral centers; // and /\ for double bonds) and SDFiles (wedge symbols in the bond block; parity flags in the atom block). Furthermore, CORINA is able to interpret input 3D structures and to determine the correct stereo chemistry from the 3D information.

The best way to cite CORINA is

(a) 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.
(http://dx.doi.org/10.1021/ci00020a039)
(b) The 3D structure generator CORINA is available from Molecular Networks GmbH, Erlangen, Germany (http://www.molecular-networks.com).

ROTATE checks all conformations for non-bonded interactions and removes those having close contacts (or atom bumps) automatically.

ROTATE can combine similar conformations into classes and represent each class by a single conformation (class representative). Two different and adjustable similarity criteria can be chosen. One crierion works in Cartesian space, i.e., is based on the RMS(XYZ) (root mean square) deviation of the Cartesian coordinates of all non-hydrogen atoms of the conformations. The second criterion uses the torsion angle space to calculate whether two conformations are similar or not, i.e., the comparison is based on the RMS(TA) deviation of the torsion angles along the rotated bonds of two conformerations.
For both methods, the RMS threshold that is used to define two conformations as similar, can be chosen by the user and both methods provide a balanced sampling of the conformational space.

ROTATE does not use a classical force field algorithm for optimization, but applies a symbolic (or empirical) energy function. This symbolic energy function is derived from the torsion angle library (TAL) that contains the
distribution of torsion angles of over 1,000 four-atomic torsion angle patterns.
The distributions are stored in histogram (from 0 to 360 degree). The frequencies of the individual torsion angle values are used to derive a symbolic energy value for each torsion angle value for a specific torsion angle pattern and a gradient optimizer identifies the minimas.

ROTATE uses a knowledge base of preferred torsion angles of acyclic, rotatable bonds (or rotors). These torsion angles have been derived from a statistical analysis of the conformational preferences of open-chain portions
in small molecule crystal structures xray taken from the CSD system (Cambridge Structural Database) and are stored in the so-called torsion angle library (TAL). Therefore, ROTATE does not perform a "classical" systemic and exhaustive search, but exhaustively searches in this space of allowed torsion angles spanned by the TAL and the generated conformations are biased towards xray geometries.

The best way to cite ROTATE is

(a) Renner, S.; Schwab, C.H.; Schneider, G.; Gasteiger, J.
Impact of conformational flexibility on three-dimensional similarity searching using correlation vectors.
J. Comp. Inf. Model. 2006, 46, 2324-2332.
(http://dx.doi.org/10.1021/ci050075s)
(b) The conformer generator ROTATE is available from Molecular Networks GmbH, Erlangen, Germany (http://www.molecular-networks.com).