Diversity assessment

Mason, J. S., Hermsmeier, M. A. Diversity assessment. Curr. Opin. Chem. Biol. 1999, 3, 342-349. 

Nilakantan, R., Bauman, N. and Haraki, K.S. Database diversity assessment new ideas, concepts and tools. J. Comput-AidedMol. Des., 1997,11,447-452. 

Lin, S.K. Molecular diversity assessment logarithmic relations ofinformation and species diversity and logarithmic relations of entropy and indistinguishability after rejection ofGibbs paradox of entropy mixing. Molecules, 1996,1, 57-67. 

An alternative methodology based on the ringcontent of a database, using precalculated structure-based hash codes has been proposed (110). The comparison of the hashcode tables can be used to compare two databases and the number of distinct ring-system combinations can be used as an indicator of database diversity. A method for diversity assessment called the saturation diversity approach, based on picking as many mutually dissimilar compounds as possible from a database was also proposed. The methods were used to compare a number of public databases and gave similar results. 

A design module will provide the capability to select the compounds and the method by which they will be synthesized. In order to perform this task, the design module must be linked to external databases that can provide data about the availability of chemical reagents and information about synthetic methods. Once the products are selected and the synthetic method selected, this information will be collated in the reaction workbook. The function of the design module is complementary to diversity assessment tools. 

Some of the most elegant work in data reduction for natural products screening has been reported in the area of diversity assessment, as discussed earlier [10]. Several of these examples involve LC/UV/MS analysis of natural product extracts on an extremely large scale. The resulting data were converted to the netCDF format and evaluated with customized software. Three-dimensional images were generated for the visualization of sample component differences, and a measure of similarity was calculated to allow for diversity assessment. This approach was also applied to the automahe deconvoluhon of the mass spectra of secondary metabolites from LC-MS data with factor analysis [117]. 

On the other hand, differences in mapping and clustering algorithms have only a minor influence on the result, and may be apphed as black boxes . The results of diversity assessment and similarity computation can provide valuable information about combinatorial libraries at an early stage (even before synthesis). This information helps the chemist to select certain building blocks or libraries. 

Diversity Assessment for Selection of Building Blocks or Compounds... 

Balian, E.V., Segers, H., L v que, C., Martens, K. (2008). Freshwater animal diversity assessment an introduction to the Freshwater Animal Diversity Assessment (FADA) project. Hydrobiologia 595,3-8. 

Chemomformattcs.org This is a norrcorrrmercial website which compiles information on chemoinformatics web resormces arrd provides links to chemoinformatics programs. It also pro ddes datasets for QSAR, QSPR, BBB penetration, CaCOj penneability, etc. There are a total of 44 datasets, which are freely downloadable. It also provides links to molecular sirrrilarity search, online diversity assessment. The datasets are divided according to the rrse irrto binary (active/inactive) datasets, QSAR datasets, QSPR datasets, toxicity datasets, metabolism datasets, permeability datasets, docking datasets, mechanistic datasets, and nrixed/other datasets. 

Techniques do exist for estimating software failure rates based on historical use data (Adelard, 2001) and work has been performed using Bayesian Belief Networks (Strigini, 1996) enabling evidence from diverse assessment activities to be combined. However, historic data cannot, obviously, be used for newly written software. 

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