Attracting Cavities 3.0: Faster and More Versatile Molecular Docking for the SwissDock Webserver

Abstract Motivation Molecular docking is a pillar of structure-based drug design and shows advantages in structure prediction of small-molecule ligand–protein complexes over co-folding methods for novel ligands and novel binding pockets. Here, we describe substantial improvements of our physics-based docking algorithm Attracting Cavities, which is widely used through the SwissDock webserver. Results AC 3.0 includes enhanced sampling features, new functionalities, and technical improvements. These lead to better sampling at lower execution times and higher versatility. Comparison with AutoDock Vina demonstrates better docking results on multiple test sets. Availability AC 3.0 will be made available free of charge through the SwissDock webserver ( www.swissdock.ch ).