PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow

Ammar Ammar, Rachel Cavill, Chris Evelo, Egon Willighagen
2022 Journal of Cheminformatics  
AbstractA key concept in drug design is how natural variants, especially the ones occurring in the binding site of drug targets, affect the inter-individual drug response and efficacy by altering binding affinity. These effects have been studied on very limited and small datasets while, ideally, a large dataset of binding affinity changes due to binding site single-nucleotide polymorphisms (SNPs) is needed for evaluation. However, to the best of our knowledge, such a dataset does not exist.
more » ... , a reference dataset of ligands binding affinities to proteins with all their reported binding sites' variants was constructed using a molecular docking approach. Having a large database of protein–ligand complexes covering a wide range of binding pocket mutations and a large small molecules' landscape is of great importance for several types of studies. For example, developing machine learning algorithms to predict protein–ligand affinity or a SNP effect on it requires an extensive amount of data. In this work, we present PSnpBind: A large database of 0.6 million mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow. It provides a web interface to explore and visualize the protein–ligand complexes and a REST API to programmatically access the different aspects of the database contents. PSnpBind is open source and freely available at https://psnpbind.org.
doi:10.1186/s13321-021-00573-5 pmid:35227289 pmcid:PMC8886843 fatcat:mac7atc7kzb4hk7lbimzzkd5z4