Fast Docking on Graphics Processing Units via Ray-Casting
By Karen R. Khar, Lukasz Goldschmidt, John Karanicolas. 2013
12 citations recorded by the source corpus.
Docking Approach using Ray Casting (DARC) is structure-based computational method for carrying out virtual screening by docking small-molecules into protein surface pockets. In a complementary study we find that DARC can be used to identify known inhibitors from large sets of decoy compounds, and can identify new compounds that are active in biochemical assays. Here, we describe our adaptation of DARC for use on Graphics Processing Units (GPUs), leading to a speedup of approximately 27-fold in typical-use cases over the corresponding calculations carried out using a CPU alone. This dramatic speedup of DARC will enable screening larger compound libraries, screening with more conformations of each compound, and including multiple receptor conformations when screening. We anticipate that all three of these enhanced approaches, which now become tractable, will lead to improved screening results.
Subfields: Computational Theory and Mathematics, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Computational Theory and Mathematics
- Ragul Gowthaman
- Sergey Lyskov
- Stefano Moro
- John Karanicolas
- Veronica Salmaso
- Luca Pinzi
- Giulio Rastelli
In Molecular Biology
- Sergey Lyskov
- Ragul Gowthaman
- Stefano Moro
- John Karanicolas
- Veronica Salmaso
- Rhiju Das
- Jeffrey J. Gray
- Tanja Kortemme
Citations in the corpus
- Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, background): “For this reason, together with few preliminary applications in the field of molecular docking ( Korb et al., 2011; Khar et al., 2013), GPUs have been mainly exploited for MD simulations, which can be parallelized at the level of atoms.”
- DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites (2015, methodology): “We find an average speedup of 90-fold when using the GPU (red line), an improvement over the 27-fold speedup we achieved in our original GPU implementation of DARC [26].”