Software CORINA

Corina Software for the generation of high-quaUty three-dimensional molecular models, by Sadowski, J., Schwab C. H., Gasteiger J. Molecular Networks GmbH Computerchemie, www.mol-net.de, Erlangen, Germany, 2004. 

The first task was the aeation of large 3D chemical structure databases. By devising so-called fast Automatic 3D model builder, software such as the CORINA [27, 28] and CONCORD [29, 30] programs resulted in a boom in 3D database development (see Section 2.9 in this book and Chapter II, Section 7.1 in the Handbook). A subsequent step was the development of fast... 

A set of n = 209 polycyclic aromatic compounds (PAC) was used in this example. The chemical structures have been drawn manually by a structure editor software approximate 3D-structures including all H-atoms have been made by software Corina (Corina 2004), and software Dragon, version 5.3 (Dragon 2004), has been applied to compute 1630 molecular descriptors. These descriptors cover a great diversity of chemical structures and therefore many descriptors are irrelevant for a selected class of compounds as the PACs in this example. By a simple variable selection, descriptors which are constant or almost constant (all but a maximum of five values constant), and descriptors with a correlation coefficient >0.95 to another descriptor have been eliminated. The resulting m = 467 descriptors have been used as x-variables. The y-variable to be modeled is the Lee retention index (Lee et al. 1979) which is based on the reference values 200, 300, 400, and 500 for the compounds naphthalene, phenanthrene, chrysene, and picene, respectively. 

CORINA www2.chemie.uni-erlangen.de/software/corina/corina.html... 

Corina http //www2.chemie.uni-erlangen.de/software/corina/free struct.html Omicron (OpenEye) http //www.eyesopen.com/products/toolkits/omicron.html BioMedCache (Cache Fujitsu) http //www.cachesoftware.com/biomedcache/ Accelrys http //www.accelrys.com... 

A descriptor for the three-dimensional arrangement of a molecule can be derived from the Cartesian coordinates of the atoms. Reliable coordinates can be calculated quite easily by semiempirical or molecular mechanics (i.e., force-field) methods by using molecular modeling software. Fast 3D structure generators are available that combine rules and force-field methods to calculate Cartesian coordinates from the connection table of a molecule (e.g., CORINA [33]). 

The ligand molecules are taken from a compound databases typically containing only structural formulae of the individual molecules. In order to use them in a docking calculation, 3D structures of the molecules have be generated. For this step, very powerful tools like Concord [166] or Corina [68, 69] exist. In addition, atom hybridization and protonation as well as bond types have to be determined. Typically, this task is performed by a series of subsequently executed rule-based scripts. It should be noted that due to the complexity of this task, the resulting structures are not free of errors in the assignment of atom and bond types. The docking software should therefore rely as little as possible on this information. 

CORINA is available firom Molecular Networks GmbH, Nagelsbachstr. 25, 91052 Erlangen, Germany, (http //www.mol-net.de) and can be tested via the internet at http //www2.chemie.uni-erlangen.de/ software/corina. 

Corina CORINA (COoRdINAtes) is a rule and data based system that automatically generates three-dimensional atomic coordinates from the constitution of a molecule as expressed by a connection table or linear code, and can convert large databases of compounds http //zabib.chemie.uni-erlangen.de/software/corina/corina.html... 

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