SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein–Ligand Poses
Adam Pecina, Susanta Haldar, Jindřich Fanfrlík, René Meier, Jan Řezáč, Martin Lepšı́k, Pavel Hobza · Journal of Chemical Information and Modeling · 2017
We have recently introduced the “SQM/COSMO” scoring function which combines a semiempirical quantum mechanical description of noncovalent interactions at the PM6-D3H4X level and the COSMO implicit model of solvation. This approach outperformed standard scoring functions but faced challenges with a metalloprotein featuring a Zn 2+ ···S – interaction. Here, we invoke SCC-DFTB3-D3H4, a higher-level SQM method, and observe improved behavior for the metalloprotein and high-quality results for the other systems. This method holds promise for diverse protein–ligand complexes including metalloproteins.