ArticleMethods in molecular biology (Clifton, N.J.)2025
Exploring Binding Sites on Proteins for Function Prediction Using the PoSSuM Databases.
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Abstract
Protein function is strongly associated with molecules with which it can interact. Using information on the accumulated complex structures of proteins and their ligands is expected to be useful for the prediction of biological functions and for drug discovery and development. To take advantage of these opportunities, we have constructed and released the PoSSuM database, with compiled similarity search results for known and putative binding sites, based on three-dimensional structures of proteins. We have also provided a database called PoSSuMds, with compiled similarity search results for drug binding sites in PoSSuM. Recently, after expanding the PoSSuM construction scheme, we have developed and released the PoSSuMAg database for seeking similarities among antibody-binding sites (antigen), along with the PoSSuMAF database, which compiles similarity search results for known and putative binding sites in predicted structural models of human proteins by AlphaFold. This chapter presents examples of how to use the websites of these databases.
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