Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species.

ABSTRACT: We describe the formalization of the reactive docking protocol, a method developed to model and predict reactions between small molecules and biological macromolecules. The method has been successfully used in a number of applications already, including recapitulating large proteomics data sets, performing structure-reactivity target optimizations, and prospective virtual screenings. By modeling a near-attack conformation-like state, no QM calculations are required to model the ligand and receptor geometries. Here, we present its generalization using a large data set containing more than 400 ligand-target complexes, 8 nucleophilic modifiable residue types, and more than 30 warheads. The method correctly predicts the modified residue in ∼85% of complexes and shows enrichments comparable to

SUBMITTER: Bianco G 

PROVIDER: S-EPMC10756071 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature