BLT Stages

Abstract 2020-2021: THE DEVELOPMENT OF AN INTEGRATED SOFTWARE PLATFORM FOR STRUCTURE-BASED DRUG DESIGN

Structure-based drug design uses high resolution protein structure information to guide the drug development process. Instead of blind screening thousands of compounds, one uses protein structure information as a map to steer the design of novel compounds. One key step in structure-based drug design is to make protein constructs with specific protein tags that can be used for protein expression and purification studies. This design process consumes multiple days as one needs to integrate data from different resources: disease information, intellectual property information and biological information. PUXANO aims to streamline this process by the development of an integrated platform for protein sequence analysis. Aim of this traineeship is to automate the bioinformatical data analysis by data integration of different databases.

General and specific protein data are hereby extracted from several plain text bioinformatic databases (e.g. Uniprot, PDB, InterPro, … ) via REST API’s. Furthermore, protein amino acid sequence data is analyzed by specialized tools that identify secondary structures such as alpha helices and beta-sheets, glycosylation sites, membrane domain delineation, etc. Both steps are done using a python script, whereby the uniprot ID is given as input data and an easily interpretable text file is generated as an output file. The project resulted in the following positive outcome: a time reduction of 5 days into a couple of minutes. In the future this project will be continued and further developed within Puxano, thereby linking other types of data.