Database diversity

Briefly, in relational databases, diverse types of information are stored in different data tables that are connected and often embedded in an ORACLE database architecture... 

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

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. 

Database diversity (see Subheading 4) was exported from ChemDiv data-... 

The ciphered code is indicated with a defined length, i.e., a fixed hit/byte length. A hash code of 32 bits could have 2 (or 4 294 976 296) possible values, whereas one of 64 bits could have 2 values, However, due to tbe fixed length, several diverse data entries could assign the same hash code ( address collision ), The probability of collision rises if the number of input data is increased in relation to the range of values (bit length). In fact, the limits of hash coding are reached with about 10 000 compounds with 32 bits and over 100 million with 64 bits, to avoid collisions in databases [97. ... 

One of the more prominent integrated databases is provided by CAS - the Registry CAPLUS, CA, CAOLD. All of these diverse databases are based on the... 

Virtual screening allows the scope of screening to be extended to external databases. When this is done, increasingly diverse hits can be identified. The application of virtual. screening techniques before or in parallel with HTS hclp.s to reduce the assay-to-lcad attrition rate observed from HTS. In addition, virtual screening is faster and less expensive than experimental synthesis and biological testing. 

This rarity value is equated with the fraction of hits that would be returned by searching large database of diverse molecules with the full pharmacophore (all K features) or thi subset (with K—1 features) as appropriate. Labelling this fraction of hits as p(x) we nov define q x) as the fraction of the M active molecules (i.e. the molecules originally suppliet as input to the procedure) which match each of the K + possible classes. The overal configuration is scored using ... 

Currunins D J, C W Andrews, J A Benfley and M Cory 1996. Molecular Diversity in Chemical Database Comparison of Medicinal Chemistry Knowledge Bases and Databases of Commercially Availabl Compounds Journal of Chemical Information and Computer Science 36 750-763. 

Budgeting. These changes in the storage and retrieval of chemical information requite that Hbraries and information centers now consider not only what should be purchased but also what monies should be allocated for the purchase of information in nonprint formats such as CD-ROMs (compact disk read-only memory) and on-line databases. Coupled with this is budgeting for the cost of hardware and software to enable the rapid and cost-effective deHvery of needed information (15). The geometric increase in sources, both printed and on-line, has increased the role of information speciaHst as an expert in the deHvery of chemical information. Retrieval from increasingly diverse and complex sources becomes the paramount issue for searchers of chemical Hterature in the 1990s. 

Many reports have been published that address various aspects of diversity analysis in the context of chemical library design and database mining [77-84]. 

DB Turner, SM Tyrell, P Willett. Rapid quantification of molecular diversity for selective database acquisition. I Chem Inf Comput Sci 37 18-22, 1997. 

DJ Cummins, CW Andrews, JA Bentley, M Cory. Molecular diversity m chemical databases Comparison of medicinal chemistry knowledge bases and databases of commercially available compounds. I Chem Inf Comput Sci 36 750-763, 1996. 

S Wang, DW Zaharevitz, R Sharma, VE Marquez, NE Lewm, L Du, PM Blumberg, GWA Milne. The discovery of novel, stnicturally diverse protein kinase C agonists through computer 3D-database pharmacophore search. I Med Chem 37 4479-4489, 1994. 

In order to get an insight into the diversity of proteins that may contain a Rieske or Rieske-type cluster, a database search was performed in the following way. 

Over the last few years at the Flexsys laboratories in Akron, OH, data has been collected on both RPA and PICO abrasion as discussed above. In total more than 500 compounds have been tested. RPA loss modulus strain sweeps and PICO abrasion results have been collected and compiled into a database. The diversity of this database is rather broad. Many formulations based on NR,... 

When a chemistry space has been defined, a database can be mapped onto the space by assigning each molecule to a cell according to its properties and a diverse subset selected by taking one or more molecules from each cell alternatively, a focused subset can be selected by choosing compounds from a limited number of cells, for example, from the cells adjacent to a cell occupied by a known active. The partitioning scheme is defined independently of... 

One early step in the workflow of the medicinal chemist is to computationally search for similar compounds to known actives that are either available in internal inventory or commercially available somewhere in the world, that is, to perform similarity and substructure searches on the worldwide databases of available compounds. It is in the interest of all drug discovery programs to develop a formal process to search for such compounds and place them into the bioassays for both lead generation and analog-based lead optimization. To this end, various similarity search algorithms (both 2D and 3D) should be implemented and delivered directly to the medicinal chemist. These algorithms often prove complementary to each other in terms of the chemical diversity of the resulted compounds [8]. 

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