SweepANN cuts day-long drug-screening retrieval to 61 seconds in tests

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SweepANN accelerates the retrieval step used to find molecules for protein pockets, the binding sites a drug targets. Researchers report cutting a full query round from roughly 24 hours to about a minute.

Here's how it works:

• The reported run searched roughly 500 million molecule vectors for more than 26,000 protein pockets in 61.04 seconds.
• Each pocket received the top 500,000 candidates, with 99.63% average recall across the run.
• Batches of 64 pockets share each vector-shard read, with matrix multiplication for scoring and temporary thresholds to avoid sorting the full score matrix.
• INT8 quantization cuts storage from about 1.54 TB to roughly 387 GB across four RTX PRO 6000 Blackwell GPUs.

One catch: the 61-second run excludes about 502 seconds for quantization and loading. That setup cost can be spread across repeated searches when the molecular library does not need re-encoding.

Sources: hyper.ai