PROBE uses edit-response probing to build site maps and EditManuals that guide multi-agent LLM optimization, achieving SOTA performance on CrossDocked2020 while mitigating joint-improvement failures.
Benchmarking generated poses: How rational is structure-based drug design with generative models?arXiv preprint arXiv:2308.07413
4 Pith papers cite this work. Polarity classification is still indexing.
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GeoCoupling optimizes temporal couplings between modalities in biomolecular generative models and outperforms synchronous baselines on drug design and protein design tasks.
DEPPA reformulates the denoising process of pocket-aware diffusion models as a multi-step MDP and applies RL fine-tuning with a coarse scheduler to optimize ligands for binding affinity, drug-likeness, synthesizability and diversity on CrossDocked2020.
EDMolGPT generates molecules from low-resolution electron density for de novo structure-based drug design, claiming better performance than pocket-based methods on 101 targets.
citing papers explorer
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Probe Before You Edit: Probing-Guided Molecular Optimization for LLM Agents in Structure-Based Drug Design
PROBE uses edit-response probing to build site maps and EditManuals that guide multi-agent LLM optimization, achieving SOTA performance on CrossDocked2020 while mitigating joint-improvement failures.
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Demystifying Multimodal Biomolecular Co-design With Intrinsic Geodesic Coupling
GeoCoupling optimizes temporal couplings between modalities in biomolecular generative models and outperforms synchronous baselines on drug design and protein design tasks.
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Fine-tuning Pocket-Aware Diffusion Models via Denoising Policy Optimization
DEPPA reformulates the denoising process of pocket-aware diffusion models as a multi-step MDP and applies RL fine-tuning with a coarse scheduler to optimize ligands for binding affinity, drug-likeness, synthesizability and diversity on CrossDocked2020.
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From Holo Pockets to Electron Density: GPT-style Drug Design with Density
EDMolGPT generates molecules from low-resolution electron density for de novo structure-based drug design, claiming better performance than pocket-based methods on 101 targets.