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António J M Ribeiro
António J M Ribeiro
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Protein-ligand docking in the new millennium–a retrospective of 10 years in the field
SF Sousa, AJM Ribeiro, JTS Coimbra, RPP Neves, SA Martins, N Moorthy, ...
Current medicinal chemistry 20 (18), 2296-2314, 2013
2662013
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites
AJM Ribeiro, GL Holliday, N Furnham, JD Tyzack, K Ferris, JM Thornton
Nucleic acids research 46 (D1), D618-D623, 2018
1732018
Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms
SF Sousa, AJM Ribeiro, RPP Neves, NF Brás, NM Cerqueira, ...
Wiley Interdisciplinary Reviews: Computational Molecular Science 7 (2), e1281, 2017
161*2017
A global analysis of function and conservation of catalytic residues in enzymes
AJM Ribeiro, JD Tyzack, N Borkakoti, GL Holliday, JM Thornton
Journal of Biological Chemistry 295 (2), 314-324, 2020
872020
Emerging concepts in pseudoenzyme classification, evolution, and signaling
AJM Ribeiro, S Das, N Dawson, R Zaru, S Orchard, JM Thornton, ...
Science Signaling 12 (594), eaat9797, 2019
852019
Benchmarking of DFT functionals for the hydrolysis of phosphodiester bonds
AJM Ribeiro, MJ Ramos, PA Fernandes
Journal of Chemical Theory and Computation 6 (8), 2281-2292, 2010
842010
Enzymatic flexibility and reaction rate: a QM/MM study of HIV-1 protease
AJM Ribeiro, D Santos-Martins, N Russo, MJ Ramos, PA Fernandes
Acs Catalysis 5 (9), 5617-5626, 2015
802015
PDBe-KB: a community-driven resource for structural and functional annotations
M Varadi, J Berrisford, M Deshpande, SS Nair, A Gutmanas, D Armstrong, ...
Nucleic Acids Research 48 (D1), D344-D353, 2020
752020
The catalytic mechanism of HIV-1 integrase for DNA 3′-end processing established by QM/MM calculations
AJM Ribeiro, MJ Ramos, PA Fernandes
Journal of the American Chemical Society 134 (32), 13436-13447, 2012
622012
Unique triphenylphosphonium derivatives for enhanced mitochondrial uptake and photodynamic therapy
Z Hu, Y Sim, OL Kon, WH Ng, AJM Ribeiro, MJ Ramos, PA Fernandes, ...
Bioconjugate Chemistry 28 (2), 590-599, 2017
602017
The catalytic mechanism of protein phosphatase 5 established by DFT calculations
AJM Ribeiro, ME Alberto, MJ Ramos, PA Fernandes, N Russo
Chemistry–A European Journal 19 (42), 14081-14089, 2013
502013
Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases
AT Pereira, AJM Ribeiro, PA Fernandes, MJ Ramos
International Journal of Quantum Chemistry 117 (18), e25409, 2017
372017
Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes
SF Sousa, GRP Pinto, AJM Ribeiro, JTS Coimbra, PA Fernandes, ...
Journal of Computational Chemistry 34 (24), 2079-2090, 2013
352013
Improving the biodesulfurization of crude oil and derivatives: a qm/mm investigation of the catalytic mechanism of NADH-FMN oxidoreductase (DszD)
SF Sousa, JFM Sousa, ACC Barbosa, CE Ferreira, RPP Neves, ...
The Journal of Physical Chemistry A 120 (27), 5300-5306, 2016
322016
New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models
GP Pinto, AJM Ribeiro, MJ Ramos, PA Fernandes, M Toscano, N Russo
Archives of biochemistry and biophysics 582, 107-115, 2015
322015
Insight into enzymatic nitrile reduction: QM/MM study of the catalytic mechanism of QueF nitrile reductase
AJM Ribeiro, L Yang, MJ Ramos, PA Fernandes, ZX Liang, H Hirao
ACS Catalysis 5 (6), 3740-3751, 2015
322015
Synthesis and Hydrolytic Studies on the Air-Stable [(4-CN-PhO)(E)P(μ-NtBu)]2 (E = O, S, and Se) Cyclodiphosphazanes
YX Shi, RZ Liang, KA Martin, N Weston, S Gonzalez-Calera, R Ganguly, ...
Inorganic Chemistry 54 (13), 6423-6432, 2015
282015
HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015)
EF Oliveira, D Santos-Martins, AM Ribeiro, NF Brás, NS Cerqueira, ...
Expert opinion on therapeutic patents 26 (11), 1257-1272, 2016
242016
Conformational variation in enzyme catalysis: a structural study on catalytic residues
IG Riziotis, AJM Ribeiro, N Borkakoti, JM Thornton
Journal of Molecular Biology 434 (7), 167517, 2022
212022
Ranking enzyme structures in the PDB by bound ligand similarity to biological substrates
JD Tyzack, L Fernando, AJM Ribeiro, N Borkakoti, JM Thornton
Structure 26 (4), 565-571. e3, 2018
202018
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