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Updated: May 17, 2026
Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
Published on: December 1, 2020
Significance estimation for sequence-based chemical similarity searching (PhAST) and application to AuroraA kinase
Volker Hähnke1, Nickolay Todoroff, Tiago Rodrigues
1Swiss Federal Institute of Technology, Department of Chemistry & Applied Biosciences, 8093 Zürich, Switzerland.
Background:
Chemical similarity searching allows the retrieval of preferred screening molecules from a compound database. Candidates are ranked according to their similarity to a reference compound (query). Assessing the statistical significance of chemical similarity scores helps prioritizing significant hits, and identifying cases where the database does not contain any promising compounds.
Method:
Our text-based similarity measure, Pharmacophore Alignment Search Tool (PhAST), employs pair-wise sequence alignment. We adapted the concept of E-values as significance estimates and employed a sampling technique that incorporates the principle of importance sampling in a Markov chain Monte Carlo simulation to generate distributions of random alignment scores. These distributions were used to compute significance estimates for similarity scores in a preliminary prospective virtual screen for inhibitors of Aurora A kinase.
Conclusion:
Assessing the significance of compound similarity computed with PhAST allows for a statistically motivated identification of candidate screening compounds. Inhibitors of Aurora A kinase were retrieved from a large compound library.
