Bioptic -- A Target-Agnostic Potency-Based Small Molecules Search Engine

• URL: http://arxiv.org/abs/2406.14572v3
• Date: Mon, 1 Jul 2024 01:33:10 GMT
• Title: Bioptic -- A Target-Agnostic Potency-Based Small Molecules Search Engine
• Authors: Vlad Vinogradov, Ivan Izmailov, Simon Steshin, Kong T. Nguyen,
• Abstract summary: We develop a target-agnostic, efficacy-based molecule search model. We screen the ultra-large 40B Enamine REAL library with 100% recall rate. We benchmarked our model and several state-of-the-art models for both speed performance and retrieval quality of novel molecules.
• Score: 0.0
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: 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.

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