Software CONCORD

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... 

The process of data collection at the installation level could be positively evaluated. It reached 2% concordance with evaluation at the macro level. The software tools used, formal procedures, and wide support of the process by detailed instructions, consultations, meetings and the WWW proved their usefulness. 

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. 

Mass spectrometric conditions Mass spectrometric analyses were accomplished on Applied Biosystems MDS Sciex (Concord, Ontario, Canada) API 2000 triple quadrupole mass spectrometer equipped with au electrospray ionization (ESI) interface. ESI was performed in the positive ionization mode. Data acquisition and processing were accomplished using the Applied Biosystans Analyst version 1.4.2 software. 

In case of nanostructure interaction with the medium molecules, the medium self-oiganization is effective with the proximity or concordance of the oscillations of separate fragments of nanostructures and chemical bonds of the medium molecules. This hypothesis of nanostructure influence on media selforganization was already discussed [10-13]. At the same time, it is possible to use quantum-chemieal eomputational experiment with the known software products. 

The FS (not shown) represents the File Segment field. It indicates the presence or absence of CONCORD 3-D co-ordinates for displaying and modelling structures using Alchemy software. Between 40% and 50% of the structures have 3-D coordinates. 

D (three-dimensional) structures. Three-dimensional coordinates have now been added to the connection tables to nearly six million organic substances using Pearlman s CONCORD software provided by Tripos Associates. These 3D structures, an example of which appears in Figure 17, are available on a retrieval basis from the Registry File on STN. 

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