COBRA database

Fig. 3.5 Averaged enrichment factors over 10 ligand classes from the COBRA database (top 5%). Comparison of the performances of MACCS, CATS, CATS3D and SURFCATS for full molecular representations, scaffolds (Sc)...

An example may help to clarify this statement Figure 13.4 shows the 10 highest-ranking compounds that were retrieved from the COBRA database by a topological pharmacophore similarity search (CATS method, see below). The query structure was Haloperidol, a dopamine (D2) receptor antagonist. Not surprisingly classic variations of the query structure are found in ranks 1 and 2. These are not very... 

Figure 6.24 Some of the most common atom-based scaffolds exclusively found in a database search of druglike compounds (COBRA), pure natural products (PNP), and marine natural products (MNP). (Grabowski, K., Schneider, G. Properties and architecture of drugs and natural products revisited. Curr. Opin Chem. Biol 2007, 1, 115-127.)...

Ricketts, E.M. Rradshaw, J. Hann, M. Hayes, F. Tanna, N. Ricketts. D.M. Comparison of conformations of small-molecule structures from the Protein Data-Bank with those generated by concord, cobra, chemdbs-3D, and converter and those extracted from the Cambridge Structural Database. J. Chem. Inf. Comput. Sci. 1993, 33. 905-925. 

E. M. Ricketts,/. Bradshaw, M. Hann,F. Hayes,N.Tanna, and D. M. Ridketts,/. Chem. Inf. Comput. Set., 33, 905 (1993). Comparison of Conformations at Small Molecules from the Protein Data Bank with Those Generated by Concord, Cobra, ChemDBS-3D and Converter, and Those Extracted from die Cambridge Structural Database. 

After the present conference ended, the author learned (Ricketts, D.M. personal communication, June 7, 1990) that program COBRA, marketed by Oxford Molecular, can generate multiple low-energy conformations from two-dimensional constitutional formula. The problem remains that if all low-energy conformations are stored, the database may become excessively large if, on the other hand, the multiple conformation search is carried out on the fly (i.e. the conformations are generated as the search proceeds) the demand for CPU capacity may be excessive. 

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