| Best Practices for Alchemical Free Energy Calculations [Article v1. 0] ASJS Mey, BK Allen, HEB Macdonald, JD Chodera, DF Hahn, M Kuhn, ... Living Journal of Computational Molecular Science 2 (1), 18378, 2020 | 173 | 2020 |
| Towards chemical accuracy for alchemical free energy calculations with hybrid physics-based machine learning/molecular mechanics potentials DA Rufa, HE Bruce Macdonald, J Fass, M Wieder, PB Grinaway, ... BioRxiv, 2020.07. 29.227959, 2020 | 72 | 2020 |
| COVID moonshot: open science discovery of SARS-CoV-2 main protease inhibitors by combining crowdsourcing, high-throughput experiments, computational simulations, and machine … H Achdout, A Aimon, E Bar-David, H Barr, A Ben-Shmuel, J Bennett, ... BioRxiv, 2020 | 53 | 2020 |
| Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo GA Ross, HE Bruce Macdonald, C Cave-Ayland, AI Cabedo Martinez, ... Journal of chemical theory and computation 13 (12), 6373-6381, 2017 | 44 | 2017 |
| Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [article v1. 0] DF Hahn, CI Bayly, ML Boby, HEB Macdonald, JD Chodera, V Gapsys, ... Living journal of computational molecular science 4 (1), 2022 | 42 | 2022 |
| Water molecules at protein–drug interfaces: computational prediction and analysis methods ML Samways, RD Taylor, HEB Macdonald, JW Essex Chemical Society Reviews 50 (16), 9104-9120, 2021 | 38 | 2021 |
| Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations HE Bruce Macdonald, C Cave-Ayland, GA Ross, JW Essex Journal of chemical theory and computation 14 (12), 6586-6597, 2018 | 37 | 2018 |
| Open Science Discovery of Potent Non-Covalent SARS-CoV-2 Main Protease Inhibitors COVID Moonshot Consortium, H Achdout, A Aimon, DS Alonzi, R Arbon, ... BioRxiv, 2020.10. 29.339317, 2020 | 36 | 2020 |
| grand: A Python Module for Grand Canonical Water Sampling in OpenMM ML Samways, HE Bruce Macdonald, JW Essex Journal of Chemical Information and Modeling 60 (10), 4436-4441, 2020 | 28 | 2020 |
| End-to-end differentiable construction of molecular mechanics force fields Y Wang, J Fass, B Kaminow, JE Herr, D Rufa, I Zhang, I Pulido, M Henry, ... Chemical science 13 (41), 12016-12033, 2022 | 24 | 2022 |
| Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors ML Boby, D Fearon, M Ferla, M Filep, L Koekemoer, MC Robinson, ... Science 382 (6671), eabo7201, 2023 | 21 | 2023 |
| Rimantadine Binds to and Inhibits the Influenza A M2 Proton Channel without Enantiomeric Specificity JL Thomaston, ML Samways, A Konstantinidi, C Ma, Y Hu, ... Biochemistry 60 (32), 2471-2482, 2021 | 16 | 2021 |
| Prediction of the closed conformation and insights into the mechanism of the membrane enzyme LpxR GM Saunders, HEB Macdonald, JW Essex, S Khalid Biophysical journal 115 (8), 1445-1456, 2018 | 6 | 2018 |
| Polymorphism in crystals of bis (4-bromophenyl) fumaronitrile through vapour phase growth TT Jensen, J Potticary, LR Terry, HEB Macdonald, JG Brandenburg, ... CrystEngComm 19 (48), 7223-7228, 2017 | 4 | 2017 |
| Water Networks in Complexes between Proteins and FDA-Approved Drugs ML Samways, HE Bruce Macdonald, RD Taylor, JW Essex Journal of Chemical Information and Modeling 63 (1), 387-396, 2022 | 2 | 2022 |
| Open Science Discovery of Oral Non-Covalent SARS-CoV-2 Main Protease Inhibitor Therapeutics (preprint) H Achdout, A Aimon, E Bar-David, H Barr, A Ben-Shmuel, J Bennett, ... | | 2020 |
| COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine … H Achdout, A Aimon, E Bar-David, H Barr, A Ben-Shmuel, J Bennett, ... bioRxiv, 2020 | | 2020 |
| The role of water in drug binding: calculating positions and binding free energies of active site water molecules, and their influence on ligand binding H Bruce Macdonald University of Southampton, 2018 | | 2018 |
| Adaptive sampling for alchemical free energy calculations and applications for drug design HE Bruce Macdonald, DA Rufa, PB Grinaway, JD Chodera | | |
Jonathan EssexProfessor of Computational Systems Chemistry, University of SouthamptonVerified email at soton.ac.uk
