Faster simulations of molecular docking processes

Through the oneAPI center, the Embedded Systems and Applications Group in collaboration with Intel will port an accelerated version of the Autodock application to create a single codebase that can be efficiently optimized and tuned for multiple hardware architecture targets.

AutoDock is widely-used for simulating molecular interactions at close distances, aiming to predict the best “fit” of two molecules to each other from a biophysical standpoint. These “docking” results are an important initial step for the discovery of new drugs, as the computations can be performed much more quickly than experiments using traditional “wet lab” chemistry.

However, the high-accuracy simulation of these docking processes is computationally expensive, and drug discovery requires the simulation of a multitude of compounds. To address this challenge, Dr. Leonardo Solis-Vasquez in the Embedded Systems and Applications Group led by Professor Andreas Koch is working on an accelerated version of AutoDock called Autodock-GPU, which aims to speedup such simulations by parallel execution utilizing a number of computing targets, including general compute multicore processsors (CPUs), graphics processors (GPUs), and reconfigurable compute units.

Together with Intel experts, TU Darmstadt is now working on a next-generation parallel implementation of AutoDock-GPU. This new effort will also leverage oneAPI. It enables easier integration of faster and higher-quality simulation algorithms. Using oneAPI, the new Autodock-GPU implementation also has the potential to be scaled-up for execution on the upcoming Aurora supercomputer at Argonne National Laboratory in Illinois (USA), which will rely on a mix of Intel CPUs and GPUs to provide a performance of two exaFLOPS. Combining an improved AutoDock-GPU with that much compute power will provide the deeper insights needed to address current and future challenges in medical and pharmaceutical research much faster than is possible today.

“We are excited to join the circle of other top research institutions as a newly established Intel oneAPI Center of Excellence. We look forward to collaborate with Intel’s experts to apply the huge strides oneAPI has made over other programming models to realize better and faster docking simulation tools, with the potential to scale from individual researcher’s workstations up to supercomputers,” says Professor Andreas Koch, Principal Investigator at the Intel oneAPI Center of Excellence at TU Darmstadt.

“The new oneAPI Center of Excellence is an exciting step forward for the multiarchitecture SYCL language and oneAPI,” says Joe Curley, vice president and general manager of Intel Software Products and Ecosystem division. “This collaboration with TU-Darmstadt team provides a path for medical and pharmaceutical researchers to use AutoDock-GPU productively on the hardware of their choice.