Screening small molecule databases

Stahl, M. and Schulz-Gasch, T. Practical database screening with docking tools. In Small Molecule-Protein Interaction, Waldmann, H. and Koppitz, M. (Eds.). Springer-Verlag, Berlin and Heidelberg, 2003, 127-150. 

David, G. (2005) Covell Linking tumor cell cytotoxicity to mechanism of drug action An integrated analysis of gene expression, small-molecule screening and structural databases. Proteins Structure, Function, and Bioinformatics, 59 (3), 403-433. 

Table 8.2 S ummary of the hierarchical filtering of a database of small molecules using the pharmacophore described in Fig. 8.9 (screening 1) and Fig. 8.12 (screening 2)...

CDD Collaborative Drug Discovery Repository of small-molecule libraries of more than 300,000 compounds derived from patents, literature, and high-throughput screening data shared by academic and pharmaceutical laboratories tested against M. tuberculosis preliminary public antimalarial database from multiple sources on 30,000 public compounds (https //www.collaborativedrug.com/pages/public access)... 

A unique database is the GDB-13 database (49), which is an exhaustive enumeration of small-molecule structures containing up to 13 heavy atoms (restricted to C, H, N, O, S, P, and Cl). Although the database does not contain activity information associated with the structures, it can be used as a source of structures for virtual screening purposes (50). It is similar in nature to databases such as ZINC (51). The key difference is that the latter are all commercially available, whereas the former are completely virtual. This class of databases is useful primarily for virtual screening type methods, where the goal is to identify candidates for more in-depth study, rather than to explicitly understand SAR trends. 

Blum LC, Reymond J-L (2009) 970 million druglike small molecules for virtual screening in the chemical universe database GDB-13. J Am Chem Soc 131(25) 8732-8733... 

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