Autodock Vina (AD Vina) is a widely used and freely available software for molecular docking to predict protein-ligand interaction. However, AD Vina is limited to run in CPU environment, although it provides the parallel docking in high performance computing. Recently, GPU-accelerated computing becomes more accessible in molecular simulations such as molecular dynamics. Here, we introduce a GPU-accelerated Autodock Vina, called Viking (Standigm Vina Docking on GPU). We ported the orginal Vina code and optimized it to run on GPU environment. Based on the analysis of the Vina code, it revealed most time determining process of Vina was the “pose search” which is expected. Therefore, we re-wrote “pose search” in order to be run on GPU processor for parallelization. In the application, we performed cross-docking application to identify ligand protein interactions predictions which typically require very large docking calculation. For example, a single query ligand for the cross-docking requires more than 10K docking calculations which correspond to the number of target proteins having 3D X-ray structures. We expect the Viking has capability of docking more than 100K ligands on a single standalone computing environment which is faster than an order of magnitude of the original Autodock Vina.

GPU-accelerated autodock vina: Viking

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.