Small-molecule interaction database

Another way to predict protein-SM interactions is to assume that similar protein sequences bind similar SMs. This is a simple, yet powerful assumption, providing accurate interaction predictions, demonstrated in a number of studies. The actual implementation of this idea into a computational algorithm is limited only by human imagination and available time, so its discussion is beyond the scope of this chapter. One interesting sequence-based interaction prediction approach reported by Synder and co-workers [61] was used to create the small-molecule interaction database (SMID) (Fig. 2-12). Biologically relevant SMs were determined from three-dimensional x-ray crystal structures containing... 

Blueprint s Small-Molecule Interaction Database (SMID), 2006 http //smid.blueprint.org. 

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. 

The terms bioinformatics and cheminformatics refer to the use of computational methods in the study of biology and chemistry. Information from DNA or protein sequences, protein structure, and chemical structure is used to build models of biochemical systems or models of the interaction of a biochemical system with a small molecule (e.g., a drug). There are mathematical and statistical methods for analysis, public databases, and literature associated with each of these disciplines. However, there is substantial value in considering the interaction between these areas and in building computational models that integrate data from both sources. In the most... 

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