Bioptic -- A Target-Agnostic Potency-Based Small Molecules Search Engine
<|reference_start|>Bioptic -- A Target-Agnostic Potency-Based Small Molecules Search Engine: Recent successes in virtual screening have been made possible by large models and extensive chemical libraries. However, combining these elements is challenging: the larger the model, the more expensive it is to run, making ultra-large libraries unfeasible. To address this, we developed a target-agnostic, efficacy-based molecule search model, which allows us to find structurally dissimilar molecules with similar biological activities. We used the best practices to design fast retrieval system, based on processor-optimized SIMD instructions, enabling us to screen the ultra-large 40B Enamine REAL library with 100\% recall rate. We extensively benchmarked our model and several state-of-the-art models for both speed performance and retrieval quality of novel molecules.<|reference_end|>
@article{vinogradov2024bioptic,
    title={Bioptic -- A Target-Agnostic Potency-Based Small Molecules Search Engine},
    author={Vlad Vinogradov, Ivan Izmailov, Simon Steshin, Kong T. Nguyen},
    journal={arXiv preprint arXiv:2406.14572},
    year={2024},
    archivePrefix={arXiv},
    eprint={2406.14572},
    primaryClass={q-bio.QM cs.AI cs.IR}
}