CONCORD program

Concentration standards, 75 750-751 Concentrators, sulfuric acid, 23 787 Concentric annular reactors, 23 544 Concentric cylinder viscometer, 27 733 Concentric hemispherical analyzer (CHA), 24 103-104, 105 energy resolution of, 24 106 Conching, milk chocolate, 6 363-364 Concomitant polymorphism, 8 69 CONCORD program, 6 10 76 752 Concrete(s)... 

R. S. Pearlman, CONCORD program and User s Manual, Tripos Associates, St. Louis, MO, 1992. 

The prediction of three-dimensional chemical structure from a list of atoms in a molecule and their connectivity is a good example of a chemical problem that may be solved by an expert system. We have already seen (Fig. 9.2) how the SMILES interpreter can construct a two-dimensional representation of a structure from its one-dimensional representation as a SMILES string. The CONCORD program (CONnection table to CoORDinates) takes a SMILES string and, very rapidly, produces a three-dimensional model of an input molecule. This system is a hybrid between an expert system and a molecular mechanics program, molecular mechanics being the method by which molecular structures are minimized in most molecular modelling systems. The procedure operates as follows. 

Many of the conversion programs apply a knowledge base to construct the 3D structure. For example, the CONCORD program combines rules with... 

These sets of structures were input to the CONCORD program to obtain 3-D coordinates. It was not possible to obtain co-ordinate data for some of the structures and the 3-D data-sets were thus as follows ... 

The type of features that are typically used in our size and shape searching are generic 3D triangle and 3D tetrangle features which are derived from 3D structures generated by the CONCORD program (see Three-dimensional Structure Generation Automation). 

A widely used 3D structure generator is CONCORD [131, 132] (for a more detailed description see Chapter II, Section 7.1 in the Handbook). CONCORD is also a rule- and data-based program system and uses a simplified force field for geometry optimization, CONCORD converts structures from 2D to 3D fairly fast... 

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],... 

Rusinko A III, J M Skell, R Balducci, C M McGarity and R S Pearlman 1988. CONCORD A. Program fi the Rapid Generation of High Quality 3D Molecular Structures. St Louis, Missouri, The University < Texas at Austin and Tripos Associates. 

R. S. PeatUnan, R. Balducci, A. Rusinko, J. M. SkeU, and K. M. Smith, CONCORD A Program for Generating Three-Dimensional Coordinates, available from Tripos Associates, St. Louis, Mo. 

Markus Joachim Seibel1 Markus J Seibel, Bone Research Program, ANZAC Research Institute, The University of Sydney, Concord, NSW, Australia... 

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... 

A simple protocol was used to build the compounds compounds were modeled with the corresponding net charges, after which 2D-3D structure conversion was carried out using the program Concord [21]. The 3D dataset obtained was submitted to the VolSurf program, and principal component analysis (PCA) was applied for chemometric interpretation. No metabolic stability information was applied to the model. 

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... 

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