Assessing protein homology models with docking reproducibility

Abstract

Results of the recent Critical Assessment of Protein Structure (CASP) competitions demonstrate that protein backbones can be predicted with very high accuracy. In particular, the artificial intelligence methods of AlphaFold 2 from DeepMind were able to produce structures that were similar enough to experimental structures that many described the problem of protein prediction solved. However, for such structures to be used for drug docking studies requires precision in the placement of side chain atoms as well. Here we built a library of 1334 small molecules and examined how reproducibly they bound to the same site on a protein using QuickVina-W, a branch of the program Autodock that is optimized for blind searches. We discovered that the higher the backbone quality of the homology model the greater the similarity between the small molecule docking to the experimental and modeled structures. Furthermore, we found that specific subsets of this library were particularly useful for identifying small differences between the best of the best modeled structures. Specifically, when the number of rotatable bonds in the small molecule increased, differences in binding sites became more apparent.