5 papers
Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints
Thomas MacDougall, Maksim Kuznetsov, Roman Schutski +5
Structure-based drug design (SBDD) leverages the 3D structure of protein targets, often complemented by other spatial constraints, to generate candidate binding molecules. While di…
URSA: Chemistry-Aware Benchmark for Utilitarian Retrosynthesis Assessment
Bogdan Zagribelnyy, Ivan Ilin, Nikita Bondarev +7
Synthesis planning aiming to find pathways of reactions for a target molecule is one of the most important and challenging tasks in drug discovery. Recent progress has produced bot…
When Single Answer Is Not Enough: Rethinking Single-Step Retrosynthesis Benchmarks for LLMs
Bogdan Zagribelnyy, Ivan Ilin, Maksim Kuznetsov +10
Recent progress has expanded the use of large language models (LLMs) in drug discovery, including synthesis planning. However, objective evaluation of retrosynthesis performance re…
MMAI Gym for Science: Training Liquid Foundation Models for Drug Discovery
Maksim Kuznetsov, Zulfat Miftahutdinov, Rim Shayakhmetov +17
General-purpose large language models (LLMs) that rely on in-context learning do not reliably deliver the scientific understanding and performance required for drug discovery tasks…
BindGPT: A Scalable Framework for 3D Molecular Design via Language Modeling and Reinforcement Learning
Artem Zholus, Maksim Kuznetsov, Roman Schutski +4
Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions bet…