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RIDGE - Rapid Docking GPU Engine

RIDGE (Rapid Docking GPU Engine) is an extremely fast and accurate structure-based virtual ligand screening method. Watch Eugene Raush's (Principal Developer, Molsoft) presentation about RIDGE at MolSoft's UGM here .

  • ~100 compounds/sec docking speed (RTX 4090)
  • ~1000 times faster than single CPU core
  • Screen 10M compounds in less than 30 hours on a single $4K desktop
  • Equivalent to 1000 core CPU cluster
  • Supports multiple GPUs
RIDGE combines MolSoft's experience and knowledge in GPU programming to create a docking engine that fully runs on the GPU. The central part of the engine is fully RAM and GPU optimized, and it also utilizes low-level CPU multithreading to ensure a balanced workload between the CPU and GPU. Additionally, it is fully compatible with existing ICM docking projects, requiring no extra setup.

The engine uses highly compressed conformer databases as input. It consists of three main blocks: the central part, which performs the docking and is fully GPU-driven; a block of CPU that handles the reading of conformers, assigning charges, and other tasks; and a final block that performs the scoring using the new neural net scoring function called RTCNN. For the final selection, an option is to apply MolSoft's ICM physics-based scoring.

In terms of benchmarks and highlights, we compared the quality of the poses with flexible ICM and found that there is less than a 10 percent loss in docking success rates for mid-sized ligands. Moreover, RIDGE achieves a high speed of approximately 100 compounds per second on a modern GPU, which is around 1,000 times faster than a single CPU core assuming a 10-second per ligand calculation. This means that you can screen 10 million compounds in less than 30 hours on a single gaming desktop, equivalent to using a one-thousand-core CPU.

RIDGE supports multiple GPUs, allowing users to split and submit jobs separately on different GPUs within their workstation. It also maintains full compatibility with existing docking projects and command line interfaces, similar to the well-known DocScan. The script name for RIDGE is "Ridge," and for its execution, you need to download and generate the conformer database.

RIDGE is available from version 393b for both Linux and Windows platforms.