3 papers
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…
physics.chem-ph2023
Accurate Free Energy Estimations of Molecular Systems Via Flow-based Targeted Free Energy Perturbation
Soo Jung Lee, Amr H. Mahmoud, Markus A. Lill
The Targeted Free Energy Perturbation (TFEP) method aims to overcome the time-consuming and computer-intensive stratification process of standard methods for estimating the free en…