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This is the fourth webinar in the BioExcel Virtual Workshop on Best Practices in QM/MM Simulation of Biomolecular Systems.

Title: Studies on enzyme-catalysed reactions

Speaker: Prof. Maria João Ramos

Thursday 10 December, 2020
15:00 CET



This talk is concerned with the computational needs that we come across to figure out results within computational enzymology. Specific problems related to the establishment of enzymatic catalytic mechanisms are put forward, as well as a way to recognise the correct one.

Single conformation QM/MM calculations, as well as multiple PES, more specifically related to the catalytic mechanism of human pancreatic alpha-amylase are reported and, at the end, averaging over an ensemble of conformations is also explained. Comparisons are made with the previously mentioned calculations. Included is also the benchmarking of density functionals that we usually carry out to find the best suited one for the system under study.

Therefore, we have resorted to different methodologies and altogether different studies [1-4] in order to analyze the energetics of processes related to the systems under study and evaluate their feasibility according to the available experimental data.


Prof. Maria João Ramos
University of Porto

Maria João Ramos gained her first degree in Chemistry at the University of Porto, a Ph.D. in Muon research as a joint project between the University of Glasgow and the then Swiss Institute for Nuclear Research (SIN), and a post-doc at the University of Oxford. In 1991 she became a Professor in Theoretical Chemistry at the University of Porto, and now heads the Theoretical and Computational Biochemistry Research Group.

Her research focuses on computational enzymatic catalysis and drug discovery, all aiming at a better understanding of the functions and applications of enzymes.

Prof. Ramos has gained the following prizes and awards: 2020, Centenary prize, University of Porto; 2019, Medinabeitia Prize, Spanish Royal Society of Chemistry (RSEQ); 2014, Honorary Doctorate, Stockholm University; 2001, Italgas Prize for Research and Technological Innovation as part of a team; 1974, Fundação Calouste Gulbenkian, Portugal, has 438 publications and an h-index of 49. She has been a consultant for national and international companies and has performed extensive evaluation research work for several research national and foreign entities. Prof. Ramos has held a number of administrative roles in her academic career including Vice-Rector for R&D, University of Porto; Director of the Science & Technology Park (UPTEC), University of Porto; Associate Director of the NFCR Centre for Computational Drug Discovery at the University of Oxford.

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[1] SF. Sousa, AJM Ribeiro, RPP Neves, NF Bras, NMFSA Cerqueira, PA. Fernandes, MJ. Ramos, WIREs, 2017, 7, 1-29.
[2] RPP. Neves, PA. Fernandes, MJ. Ramos, PNAS, 2017, 114, E4724-E4733.
[3] D. Santos-Martins, AR. Calixto, PA. Fernandes, MJ. Ramos, MJ, ACS Catalysis, 2018, 8, 4055-4063.
[4] P. Ferreira, NMFSA. Cerqueira, PA. Fernandes, MJ. Romão, MJ. Ramos, ACS Catalysis, 2020, 10, 16, 9276-9286.