Search designs

Various grid search designs to select vectors x to evaluate fix). 

Figure 2.35. Web-based chemistry search tool that combines multiple search criteria to query compound structures and related data. Uses Marvin for structure input and viewing and JChem Base for structural search, designed by Zhenbin Li of Neurogen Corporation...

D similarities (see Seet. 1.2 for details). This raises the question of whether 2-D similarities perform equally or better than 3-D methods in tasks commonly carried out in chemical informatics. Conclusive results have not been achieved to date. Nevertheless, it appears that 2-D methods can in many cases perform equally well and in some cases outperform 3-D methods [17, 18] in a variety of tasks. These tasks include similarity-based searches designed to identify new, potentially active molecules based on previously determined actives and to identify molecules with potentially similar values for properties of interest in drag research such as logP— both are examples of the SPP. In addition, these workers showed that of the 2-D methods considered molecular ACCess system (MACCS) stractural-key-based fingerprints (FPs) (yide infra) consistently exhibited the best performance. 

Haines, R. C., "Substructure Search Design Study Status Report", Chemical Abstracts Service Working Paper (unpublished), 1976. 

Similarity search appears as an extremely useful tool for computer-aided structure elucidation as well as for molecular design. Here the similarity property principle is involved. This may be stated as ... 

Similarity search appears as an extremely useful tool for computer-aided structure elucidation as well as molecular design. 

Following the similar structure - similar property principle", high-ranked structures in a similarity search are likely to have similar physicochemical and biological properties to those of the target structure. Accordingly, similarity searches play a pivotal role in database searches related to drug design. Some frequently used distance and similarity measures are illustrated in Section 8.2.1. 

Protein structure know 11 dt novo design, receptor-based 3D searching stnjcture-based design, docking... 

I J, J C Cole, J P M Lommerse, R S Rowland, R Taylor and M L Verdonk 1997. Isostar A Libraij )f Information about Nonbonded Interactions. Journal of Computer-Aided Molecular Design 11 525-531. g G, W C Guida and W C Still 1989. An Internal Coordinate Monte Carlo Method for Searching lonformational Space. Journal of the American Chemical Scociety 111 4379-4386. leld C and A J Collins 1980. Introduction to Multivariate Analysis. London, Chapman Hall, ig C-W, R M Cooke, A E I Proudfoot and T N C Wells 1995. The Three-dimensional Structure of 1 ANTES. Biochemistry 34 9307-9314. 

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