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Figure 1 | BMC Genomics

Figure 1

From: antibacTR: dynamic antibacterial-drug-target ranking integrating comparative genomics, structural analysis and experimental annotation

Figure 1

Pipeline flowchart. Each proteome of interest was subjected to the computational pipeline depicted in the flowchart. Each protein sequence is compared using BLASTPGP against: (1) the human proteome to look for similarities that could lead to toxicity, (2) other Gram-negative bacteria to estimate the evolutionary conservation, (3) its own proteome to find isoforms and paralogs that could reduce effectivity and promote resistance, (4) the database of essential genes (DEG). The results of these queries are combined into a scoring function as described in the main text. To integrate further relevant information, protein sequences are also queried against known drug targets (DrugBank) and virulence factors (VFDB). In a complementary manner, active sites are predicted as well and, if proper structural templates are found, the protein structure is modeled by homology. If the structure is modeled successfully, ligand-binding sites are predicted and analyzed as described in the main text. The pipeline’s output is a ranked list of the organism’s proteins based on the comparative genomics analysis (i.e. essentiality, evolutionary conservation, toxicity and paralogs scores) with links to external databases (VFDB and DrugBank) and when possible, to the corresponding structural modeling and analysis results.

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