CORINA program

J. Gasteiger, C. Rudolph and J. Sadowski, Tetrahedron Comp. Method. 3 (1990) 537-547 CORINA program Molecular Networks GmbH, Erlangen, Germany. 

The Corina program can generate 3D coordinates for 2D structures rapidly [61] With the help of a 3D structure, it is possible to calculate energy of the molecule, volume, interatomic charge distribution, and other 3D descriptors required for quantitative structure-activity relationship (QSAR)-based predictive studies (Fig. 1.24). 

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... 

Two of the widely used programs for the generation of 3D structures are CONCORD and CORINA. CONCORD was developed by Pearlman and co-workers (17, 18] and is distributed by TRIPOS (19). The 3D-structure generator CORINA originates from Gasteiger s research group [20-23] and is available from Molecular Networks [24],... 

This coding is performed in three steps (cf Chapter 8) First the 3D coordinates of the atoms arc calculated using the structure generator CORINA (COoRdlNAtes). Subsequently the program PETRA (Parameter Estimation for the Treatment of Reactivity Applications) is applied for calculating physicochemical properties such as charge distribution and polarizability. The 3D information and the physicochemical atomic properties are then used to code the molecule. 

Close intramolecular contacts (clashes). A rough measure has been proposed and implemented in the program CONCORD [4,11] - the close contact ratio (CCR). The CCR of a 3D stracture is defined as the ratio of the smallest nonbonded distance to the smallest acceptable value for this distance. Normally, structures with CCR>0.8 are acceptable. Some programs as CORINA [5] or CONCORD [4, 11] have fallback procedures for attempting to relax close contacts in structures with unacceptably low CCR. 

Programs. CONCORD version 6.1.0 and CORINA version 3.4 were used for this study. CONCORD was run with the following ophons ... 

Results. Table 7.1 summarizes the results of the evaluation study obtained for CONCORD and CORINA. None of the programs crashed or produced any stereo errors. CORINA had a conversion rate close to 100%, whereas CONCORD converted only 91%. However, CONCORD was faster than CORINA with an average... 

In this section a few practical recommendations are given. Most of them are generally applicable to all programs, some are specific for CORINA - the program the author of this chapter is best familiar with. 

Practically all virtual screening procedures rely at least in part on some numerical optimization, be it an optimization of overlap (as in many alignment programs) [81-90], the generation of energetically favorable conformations of a molecule (for example CONCORD ]91] and CORINA [92]), or the relaxation of a compound in complex with the protein (for example [93-97]). The particular virtual screening problem as a whole may be solved this way. Once a decent scoring function is defined, numerical methods... 

The Chemistry Development Kit (CDK) Application Programming Interface (API) (7), OpenBabel (8), or CORINA... 

Among the advantages with 2D-based descriptors are their rapid speed of computation for large sets of compounds and that they do not require 3D structures. Thus, these descriptors avoid the problem and compute times associated with 3D structure generation and conformational analysis, even though there are programs available that generate reliable 3D structures, for example, CORINA [5]. 

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