ParKVFinder: A thread-level parallel approach in biomolecular cavity detection

Abstract

Biological processes are regulated mainly by the binding of small molecules into cavities distributed throughout the biomolecular structure. Computational tools to detect these cavities have an essential role in rational drug design. With the exponential availability of high-order 3D atomic structures and large sets of atomic models, the tools must balance accuracy and speed. In this sense, we developed parKVFinder, a parallelized software for geometry-based cavity detection. Here, we described its functionalities and presented its easy-to-use PyMOL plugin and command-line interface. Finally, we demonstrated parKVFinder by identifying an important HIV-1 protease cavity and compared it with other geometry-based programs.

Keywords

• Cavity detection
• Parallelization
• Space segmentation
• Spatial characterization
• OpenMP