CONCORD, generation

Of these, 259, 124, 76, and 160 compounds respectively match the total search target. The low percentage of designed compounds that meet the total criteria was a source of concern. However, it was shown not to be due to the MODSMI transformations but rather because firstly, CONCORD generates only one conformation that might be different from that of the database molecule and secondly, the original search used broad criteria in order not to miss any interesting molecules. Each of these is responsible for approximately 50% of the failures . 

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... 

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. 

CONCORD 2-D to 3-D converters converter/conformation generator Tripos... 

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. 

As usually viewed by the reference material producers, a fundamental philosophy of certification rests on the concept of independent methodology, which is the application of theoretically and experimentally different measurement techniques and procedures to generate concordant results leading to one reliable assigned value for the property. Such assigned values are thus method-independent. Extractable concentrations are generated by specific procedures and are thus method-dependent, an idea that has to be rationalized with the fundamental method-independent concept in reference material certification work. 

The bakers yeast Saccharomyces cerevisiae represents probably the currently best researched and understood eukaryotic organism. Most of its genes have been knocked out for functional studies, and hence a vast variety of mutant strains as well as tools for their manipulation are available. This in concordance with short generation times and a growth medium that is comparable in cost and complexity to bacterial media has made the yeast system a frequent choice for the evaluation of transmembrane carriers. 

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... 

Pearlman, D.A. CONCORD rapid generation of high quality approximate 3D molecular structures. Chem. Des. Automat. News. 1987, 2, 1-7. 

Menaker You are focused on methods of analysis here. But it seems to me that if you are going to try to get concordance among experiments from different laboratories, you really have to worry about the conditions of the experiments. Michael Rosbash showed us nice data indicating that damped oscillations can grow in constant darkness in some of the cells. If you take this seriously, and you are trying to compare data sets that were generated after 1 d DD with those generated after 3 d DD, there is a problem. 

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