Binning schemes for partition-based compound selection.

Partition-based approaches to the selection of structurally diverse sets of compounds involve allocating compounds to the individual elements of a multidimensional grid that spans the available chemical space. The space is defined by an appropriate set of chemical properties, with subranges of the values of these properties being used to define the constituent elements, or bins. This article compares several binning schemes in terms of their ability to provide an even distribution of compounds across the available space and to maximise the numbers of active molecules identified in simulated assay experiments.

[1]  Jon Louis Bentley,et al.  Multidimensional Binary Search Trees in Database Applications , 1979, IEEE Transactions on Software Engineering.

[2]  Robert D. Clark,et al.  OptiSim: An Extended Dissimilarity Selection Method for Finding Diverse Representative Subsets , 1997, J. Chem. Inf. Comput. Sci..

[3]  Yvonne C. Martin,et al.  Use of Structure-Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection , 1996, J. Chem. Inf. Comput. Sci..

[4]  K. M. Smith,et al.  Novel software tools for chemical diversity , 1998 .

[5]  John Bradshaw,et al.  The Effectiveness of Reactant Pools for Generating Structurally-Diverse Combinatorial Libraries , 1997, J. Chem. Inf. Comput. Sci..

[6]  Mark P. Carpenter.  Similarity of Pratt's measure of class concentration to the Gini index , 1979, J. Am. Soc. Inf. Sci..

[7]  Jürg Nievergelt,et al.  The Grid File: An Adaptable, Symmetric Multikey File Structure , 1984, TODS.

[8]  Stephen D. Pickett,et al.  Diversity Profiling and Design Using 3D Pharmacophores: Pharmacophore-Derived Queries (PDQ) , 1996, J. Chem. Inf. Comput. Sci..

[9]  P. M. Dean,et al.  New Perspectives in Drug Design , 1995 .

[10]  James B. Dunbar,et al.  Enhancing the diversity of a corporate database using chemical database clustering and analysis , 1995, J. Comput. Aided Mol. Des..

[11]  Robert D Clark,et al.  Neighborhood behavior: a useful concept for validation of "molecular diversity" descriptors. , 1996, Journal of medicinal chemistry.

[12]  C SevcikKenneth,et al.  The Grid File , 1984 .

[13]  Ian A. Watson,et al.  Experimental Designs for Selecting Molecules from Large Chemical Databases , 1997, J. Chem. Inf. Comput. Sci..

[14]  Robin W. Spencer.  Diversity Analysis in High Throughput Screening , 1997 .

[15]  P Willett,et al.  Comparison of algorithms for dissimilarity-based compound selection. , 1997, Journal of molecular graphics & modelling.

[16]  John Bradshaw,et al.  Identification of Biological Activity Profiles Using Substructural Analysis and Genetic Algorithms , 1998, J. Chem. Inf. Comput. Sci..

[17]  Anthony W. Czarnik,et al.  A practical guide to combinatorial chemistry , 1997 .

[18]  Stephen D. Pickett,et al.  Partition-based selection , 1996 .

[19]  Robert D. Brown.  Descriptors for diversity analysis , 1996 .

[20]  Robin Taylor,et al.  Simulation Analysis of Experimental Design Strategies for Screening Random Compounds as Potential New Drugs and Agrochemicals , 1995, J. Chem. Inf. Comput. Sci..

[21]  David J. Cummins,et al.  Molecular Diversity in Chemical Databases: Comparison of Medicinal Chemistry Knowledge Bases and Databases of Commercially Available Compounds , 1996, J. Chem. Inf. Comput. Sci..

[22]  Ramaswamy Nilakantan,et al.  Database diversity assessment: New ideas, concepts, and tools , 1997, J. Comput. Aided Mol. Des..

[23]  H. Matter,et al.  Selecting optimally diverse compounds from structure databases: a validation study of two-dimensional and three-dimensional molecular descriptors. , 1997, Journal of medicinal chemistry.

[25]  Brian D. Hudson,et al.  Parameter Based Methods for Compound Selection from Chemical Databases , 1996 .