Clustering databases

D.J. Wales et al., The Cambridge Cluster Database, 2007, http //www-wales.ch.cam. ac.uk/CCD.html. A. Cuccoli, A. Macchi, V. Tognetti, R. Vaia, Monte Carlo computations of the quantum kinetic energy of rare-gas solids, Phys. Rev. B 47 (1993) 14923. 

FJ clusters (in FJ units, or as a model for specified rare-gas atom clusters) continue to be used as a benchmark system for verification and tuning in method development. With the work of Romero et al. [52], there are now proposed global minimum structures and energies available on the internet [53], up to n=309. This considerably extends the Cambridge cluster database [54], but the main body of data comes from EA work that used the known FJ lattices (icosahedral, decahedral, and face-centered cubic) as the input. This is obviously dangerous,... 

Wales DJ, Doye JPK, Dullweber A, Hodges MP, Naumkin FY, Calvo F, Hernandez-Rojas J, Middleton TF The Cambridge cluster database,http //www-wales.ch.cam.ac.uk/CCD.html... 

The new subset-selection methods draw heavily upon the techniques that are used for searching and clustering databases of two-dimensional (2D) and three-dimensional (3D) chemical structures [1-4], These techniques were... 

Graul, R. C., and Sadee, W. (2001). Evolutionary relationships among G protein-coupled receptors using a clustered database approach. AAPS PharmSci. 3, El 2. 

Search or downlo the UniProt Reference Cluster databases- UniRef coinbines dosely related sequences into a single record tg spaed sequence searches. 

The Cambridge Cluster Database, http //www-wales.ch.cam.ac.uk/CCD.html... 

Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

Downs G M, P Willett amd W Fisanick 1994. Similarity Searching and Clustering of Chemical-Stnictur Databases Using Molecular Property Data. Journal of Chemical Information and Computer Scienc 34 1094-1102. 

A cluster of databases on toxicology, hazardous chemicals and related areas, i.e. the pharmacological, biochemical, physiological, and toxicological effects of drugs and other chemicals. 

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. 

Clustering is the process of dividing a collection of objects into groups (or clusters) so that the objects within a cluster are highly similar whereas objects in different clusters are dissimilar [41]. When applied to databases of compounds, clustering methods require the calculation of all the pairwise similarities of the compounds with similarity measures such as those described previously, for example, 2D fingerprints and the Tanimoto coefficient. 

Downs GM, Willett P. Clustering of chemical structure databases for compound selection. In van de Waterbeemd H, editor, Advanced computer-assisted techniques in drug discovery. Weinheim VCH Verlag, 1994. p. 111-30. 

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