In order to execute more advanced computational chemogenomic workflows, it is essential to understand the basic data formats and options for processing them. In this chapter, de facto standards for compound and protei...
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In order to execute more advanced computational chemogenomic workflows, it is essential to understand the basic data formats and options for processing them. In this chapter, de facto standards for compound and protein representation are explained, with procedures for processing them given. A walkthrough demonstrates the step-by-step processes of downloading a ligand–target database, parsing the bioactivity in the database, automatically retrieving its chemical structures and protein sequences from a command line, and finally converting the structures and sequences into representative machine-ready formats. A basic protocol to visualize the parsed database and look for patterns is also given. less
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