Knowledge-based library

Taylor, R., Cole, J., Korb, O., McCabe, P. (2014). Knowledge-Based Libraries for Predicting the Geometric Preferences of Druglike Molecules. Journal of Chemical Information and Modeling, 54(9), 2500-2514. 

Figure 1.1 Input and output for the knowledge-based library Mogul (a) a diaryidithlole fragment Is input via the graphical interface and (b) the C-S-S-C torsion angle In the query fragment is compared instantly with all similar S-5 bonds In the CSD. Reproduced by permission of The Cambridge Crystallographic Data Centre...

Two basic uses of the CSD are to study intramolecular geometry, particularly the conformational preferences exhibited by molecules and chemical fragments, and intermolecular interactions, including hydrogen bonds and other interactions. To provide rapid click of a button access to such standard derived information, the CSD System also contains two major knowledge-based libraries. 

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... 

Knowledge-based data mining algorithms used for correlation of molecular properties with specific activities play an increasingly significant role in modern strategies of chemical library design as relatively inexpensive, yet comprehensive tools. The ability to identify compounds with the desired... 

Savchuk NP, Balakin KV. Data mining approaches for enhancement of knowledge-based content of de novo chemical libraries. In Alvarez H, Shoichet B, editors, Virtual screening in drug discovery. New York CRC Press, 2005. p. 121-49. 

Ghose, A. K., Viswanadhan, V. N., Wendoloski, J. J. A knowledge-based approach in designing combinatorial or medicinal chemistty libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases./. Comb. Chem. 1999, 1, 55-58. 

As well as purely factual data and production rules, the knowledge base may contain a section devoted to case-based information. This is a library of specific examples that in the past have proved informative and that relate to the area in which the system has expertise. 

Chose AK, Viswanadhan VN, Wendoloski JJ. (1999) A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for... 

CombiSMoG Uses a Monte Carlo ligand growth algorithm and knowledge-based potentials to combine combinatorial and rational strategies for generating biased compound libraries (86)... 

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