arXiv Machine Learning By Daria A. Ryabchenko (Ligand Pro, Moscow, Russia, Skolkovo Institute of Science and Technology, Artificial Intelligence Center, Moscow, Russia), Pavel Gurevich (Ligand Pro, Moscow, Russia, Skolkovo Institute of Science and Technology, Artificial Intelligence Center, Moscow, Russia), Shamil Kadyrov (Ligand Pro, Moscow, Russia), Daria Frolova (Ligand Pro, Moscow, Russia, Skolkovo Institute of Science and Technology, Artificial Intelligence Center, Moscow, Russia), Kseniia Fedisheva (Ligand Pro, Moscow, Russia), Sergei A. Nikolenko (Ligand Pro, Moscow, Russia), Alexander Shapeev (Ligand Pro, Moscow, Russia, Skolkovo Institute of Science and Technology, Artificial Intelligence Center, Moscow, Russia), Marina A. Pak (Ligand Pro, Moscow, Russia)

HEDGEHOG: Hierarchical Evaluation of Drug Generators Through Rigorous Filtration

Read the original on arXiv Machine Learning →

arXiv:2607. 13155v1 Announce Type: new Abstract: Generative molecular models can support early drug discovery by proposing new candidate compounds de novo.

Summary generated by The Flow from the publisher's feed. The full article lives at arXiv Machine Learning.

arXiv AI
Jul 21

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints

arXiv:2607. 18144v1 Announce Type: cross Abstract: Structure-based drug design (SBDD) leverages the 3D structure of protein targets, often complemented by other spatial constraints, to generate candidate binding molecules.

By Thomas MacDougall, Maksim Kuznetsov, Roman Schutski, Rim Shayakhmetov, Maxim Malkov, Vladimir Aladinskiy, Alex Aliper, Alex Zhavoronkov
arXiv AI
Jun 2

Probe Before You Edit: Probing-Guided Molecular Optimization for LLM Agents in Structure-Based Drug Design

arXiv:2606. 00555v1 Announce Type: new Abstract: Structure-based drug design increasingly employs LLM agents to iteratively refine ligands against a target pocket, yet a viable ligand must satisfy two often-conflicting objectives -- binding affinity and druggability -- which single optimization steps rarely improve together.

By Zaifei Yang, Weiyu Chen, Yaqing Wang, James Kwok