M. Bieniek

Computer Science · Physical Sciences

8h-index158citations34works3.12yr avg
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Research Topics

Computational Drug Discovery Methods(12), Protein Structure and Dynamics(10), Crystallization and Solubility Studies(7), X-ray Diffraction in Crystallography(7), SARS-CoV-2 and COVID-19 Research(5)

Publications34 total

ENHANCE-PET/MOOSE: moosez-v.3.1.5
Zenodo (CERN European Organization for Nuclear Research)·2026Open Access
CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13
Journal of Chemical Information and Modeling·2025· 8 citedOpen Access
CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13
2025Open Access
CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13
2025· 2 citedOpen Access
CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13
2025· 1 citedOpen Access
Evaluation of Machine Learning/Molecular Mechanics End-State Corrections with Mechanical Embedding to Calculate Relative Protein–Ligand Binding Free Energies
Journal of Chemical Theory and Computation·2025· 16 cited
Active learning driven prioritisation of compounds from on-demand libraries targeting the SARS-CoV-2 main protease
Digital Discovery·2025· 3 citedOpen Access
Author response for "Active learning driven prioritisation of compounds from on-demand libraries targeting the SARS-CoV-2 main protease"
2024
An evaluation of machine learning/molecular mechanics end-state corrections with mechanical embedding to calculate relative protein-ligand binding free energies
arXiv (Cornell University)·2024Open Access
Active learning driven prioritisation of compounds from on-demand libraries targeting the SARS-CoV-2 main protease
2024· 1 citedOpen Access
Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand–Protein Interactions and Allostery in SARS-CoV-2 Targets
Journal of Chemical Theory and Computation·2023· 22 citedOpen Access
Long timescale ensemble methods in molecular dynamics: Ligand-protein interactions and allostery in SARS-CoV-2 targets
2023Open Access
Long timescale ensemble methods in molecular dynamics: Ligand-protein interactions and allostery in SARS-CoV-2 targets
2023· 1 citedOpen Access
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal
Journal of Chemical Information and Modeling·2023· 3 citedOpen Access
Image Analysis System for Augmented Reality Games
Lecture notes in networks and systems·2023
An open-source molecular builder and free energy preparation workflow
Communications Chemistry·2022· 13 citedOpen Access
Data for FEgrow: An Open-Source Molecular Builder and Free Energy Preparation Workflow
Zenodo (CERN European Organization for Nuclear Research)·2022Open Access
Data for FEgrow: An Open-Source Molecular Builder and Free Energy Preparation Workflow
Zenodo (CERN European Organization for Nuclear Research)·2022Open Access
Data for FEgrow: An Open-Source Molecular Builder and Free Energy Preparation Workflow
Zenodo (CERN European Organization for Nuclear Research)·2022Open Access
An Open-Source Molecular Builder and Free Energy Preparation Workflow
2022· 1 citedOpen Access
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Frequent Co-authors

Ben Cree(13), Daniel J. Cole(13), Rachael Pirie(10), Joshua T. Horton(10), Natalie J. Tatum(10), Anna Makal(7), Peter V. Coveney(6), Karol Grela(6), Agastya P. Bhati(5), Oleksandra Herasymenko(4), Madhushika Silva(4), Abd Al‐Aziz A. Abu‐Saleh(4), Jesus Antonio Alvarado-Huayhuaz(4), Oscar E. A. Arce(4), Roly J. Armstrong(4), Kelly E. R. Bachta(4), Hartmut Beck(4), Dénes Berta(4), Vincent Blay(4), Albina Bolotokova(4)