3 papers
q-bio.BM2026
AgenticPosesRanker: An Agentic AI Framework for Physically Grounded Ranking of Protein-Ligand Docking Poses
Sofiene Khiari, Amr H. Mahmoud, Markus A. Lill
Scoring functions remain the principal bottleneck in molecular docking: they routinely fail to rank near-native poses above decoys, and their composite single-score design obscures…
q-bio.BM2025
Synthetic Protein-Ligand Complex Generation for Deep Molecular Docking
Sofiene Khiari, Matthew R. Masters, Amr H. Mahmoud +1
The scarcity of experimental protein-ligand complexes poses a significant challenge for training robust deep learning models for molecular docking. Given the prohibitive cost and t…
q-bio.BM2024
Accelerated Hydration Site Localization and Thermodynamic Profiling
Florian B. Hinz, Matthew R. Masters, Julia N. Kieu +2
Water plays a fundamental role in the structure and function of proteins and other biomolecules. The thermodynamic profile of water molecules surrounding a protein are critical for…