Matteo Aldeghi
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Accurate calculation of the absolute free energy of binding for drug molecules
M Aldeghi, A Heifetz, MJ Bodkin, S Knapp, PC Biggin
Chemical science 7 (1), 207-218, 2016
Two‐and Three‐dimensional Rings in Drugs
M Aldeghi, S Malhotra, DL Selwood, AWE Chan
Chemical biology & drug design 83 (4), 450-461, 2014
Predictions of ligand selectivity from absolute binding free energy calculations
M Aldeghi, A Heifetz, MJ Bodkin, S Knapp, PC Biggin
Journal of the American Chemical Society 139 (2), 946-957, 2017
Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance
O Fedorov, J Castex, C Tallant, DR Owen, S Martin, M Aldeghi, ...
Science advances 1 (10), e1500723, 2015
Large scale relative protein ligand binding affinities using non-equilibrium alchemy
V Gapsys, L Pérez-Benito, M Aldeghi, D Seeliger, H Van Vlijmen, ...
Chemical Science 11 (4), 1140-1152, 2020
The Fragment molecular orbital method reveals new insight into the chemical nature of GPCR–ligand interactions
A Heifetz, EI Chudyk, L Gleave, M Aldeghi, V Cherezov, DG Fedorov, ...
Journal of chemical information and modeling 56 (1), 159-172, 2016
Statistical analysis on the performance of Molecular Mechanics Poisson–Boltzmann Surface Area versus absolute binding free energy calculations: Bromodomains as a case study
M Aldeghi, MJ Bodkin, S Knapp, PC Biggin
Journal of chemical information and modeling 57 (9), 2203-2221, 2017
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations
A Rizzi, T Jensen, DR Slochower, M Aldeghi, V Gapsys, D Ntekoumes, ...
Journal of computer-aided molecular design 34 (5), 601-633, 2020
Data-driven strategies for accelerated materials design
R Pollice, G dos Passos Gomes, M Aldeghi, RJ Hickman, M Krenn, ...
Accounts of Chemical Research 54 (4), 849-860, 2021
A molecular mechanism for transthyretin amyloidogenesis
AW Yee, M Aldeghi, MP Blakeley, A Ostermann, PJ Mas, M Moulin, ...
Nature communications 10 (1), 1-10, 2019
Fragment molecular orbital method applied to lead optimization of novel interleukin-2 inducible T-cell kinase (ITK) inhibitors
A Heifetz, G Trani, M Aldeghi, CH MacKinnon, PA McEwan, FA Brookfield, ...
Journal of medicinal chemistry 59 (9), 4352-4363, 2016
Accurate estimation of ligand binding affinity changes upon protein mutation
M Aldeghi, V Gapsys, BL de Groot
ACS central science 4 (12), 1708-1718, 2018
Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo
M Aldeghi, GA Ross, MJ Bodkin, JW Essex, S Knapp, PC Biggin
Communications chemistry 1 (1), 1-12, 2018
Nanoparticle synthesis assisted by machine learning
H Tao, T Wu, M Aldeghi, TC Wu, A Aspuru-Guzik, E Kumacheva
Nature Reviews Materials 6 (8), 701-716, 2021
Gryffin: An algorithm for Bayesian optimization of categorical variables informed by expert knowledge
F Häse, M Aldeghi, RJ Hickman, LM Roch, A Aspuru-Guzik
Applied Physics Reviews 8, 031406, 2021
Olympus: a benchmarking framework for noisy optimization and experiment planning
F Häse, M Aldeghi, RJ Hickman, LM Roch, M Christensen, E Liles, ...
Machine Learning: Science and Technology 2 (3), 035021, 2021
Predicting kinase inhibitor resistance: physics-based and data-driven approaches
M Aldeghi, V Gapsys, BL de Groot
ACS central science 5 (8), 1468-1474, 2019
Using the fragment molecular orbital method to investigate agonist–orexin-2 receptor interactions
A Heifetz, M Aldeghi, EI Chudyk, DG Fedorov, MJ Bodkin, PC Biggin
Biochemical Society Transactions 44 (2), 574-581, 2016
Absolute alchemical free energy calculations for ligand binding: A beginner’s guide
M Aldeghi, JP Bluck, PC Biggin
Computational Drug Discovery and Design, 199-232, 2018
Assigning confidence to molecular property prediction
AK Nigam, R Pollice, MFD Hurley, RJ Hickman, M Aldeghi, N Yoshikawa, ...
Expert opinion on drug discovery 16 (9), 1009-1023, 2021
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Articles 1–20