Theoretical & Computational Biochemistry

GROUP MEMBERS 

Maria João Ribeiro Nunes Ramos (Full Professor)
Maria Natália Dias Soeiro Cordeiro (Associate Professor)
Pedro Manuel Azevedo Alexandrino Fernandes (Associate Professor)
Alexandre Lopes Magalhães  (Assistant Professor)
André Alberto de Sousa Melo  (Assistant Professor)
Nuno M. F. Sousa A. Cerqueira  (Assistant Researcher)
Sérgio Filipe Sousa  (Assistant Researcher)
Natércia Fernandes Brás  (Assistant Researcher (QREN))
N. S. Hari Narayana Moorthy  (post-doc)
Daniel José Viegas Antunes dos Santos (Assistant Researcher)
Zuzana Benkova  (post-doc)
José Luis Cagide Fajín  (post-doc)

LABs WEBSITEs
http://www.fc.up.pt/pessoas/mjramos
http://www.fc.up.pt/pessoas/ncordeir

 

RESEARCH INTERESTS AND OBJECTIVES
The Computational Chemistry and Biochemistry Research Group is formed of six PhD researchers who are also Professors at the Department of Chemistry and Biochemistry of the Faculty of Sciences of the University of Porto. They all have started their academic activities, teaching and research, in the area of theoretical chemistry. Over the last two decades, the scientific interests of the Group have evolved as a consequence of the amazing evolution in informatics and the new trends of the international scientific community. The group attracted a significant number of members, that presently amount to 4 researchers, 3 post-docs, 13 PhD students and 13 undergraduate students.
The interests of the group are now more focused on protein activity, enzymatic reaction mechanisms, improvement of computational tools and methodologies, adsorption of small species on several surfaces and heterogeneous catalysis. Concerning methodologies, the researchers have acquired expertise in high level quantum-mechanical methods (DFT, post-Hartree-Fock), classical molecular dynamics simulations, Monte Carlo simulations, Quantitative structure–activity relationship (QSAR) calculations, and hybrid QM/MM calculations.
In 1996 the Group benefited from the relocation of the Faculty of Sciences into a purpose-built building. Today, the Group occupies four computational laboratories of 42 square meters each, a room for meetings, private office rooms for the staff and researchers, and a climatized room of 24 square meters to host the computer cluster. The computational laboratories are equipped with a number of local personal computers enough for all the researchers and students, which are used both as current calculation machines and as terminals to access the computer cluster. This last equipment has been continuously updated over the years, and has reached at present time a significant computational power, resulting in the biggest national cluster for scientific purposes in Portugal.

REPRESENTATIVE PUBLICATIONS
1) António J.M.; Ramos Maria J.; Fernandes Pedro A., The Catalytic Mechanism of HIV-1 Integrase for DNA 3’-End Processing Established by QM/MM Calculations, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134, 13436–13447 (2012)

2) Oliveira  Eduardo F.; Cerqueira Nuno M. F. S. A.; Fernandes Pedro A.; Ramos Maria J., Mechanism of Formation of the Internal Aldimine in Pyridoxal 5 '-Phosphate-Dependent Enzymes, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133, 15496-15505  (2011)

3) Kuzniarska-Biernacka I; Biernacki K; Magalhaes, AL; Fonseca AM; Neves,IC; Catalytic behavior of 1-(2-pyridylazo)2-naphtol transition metal complexes encapsulated in Y zeolite, JOURNAL OF CATALYSIS, 278(1), 102-110, (2011)

4) Bras, NF; Fernandes, PA; Ramos, MJ, QM/MM Studies on the beta-Galactosidase Catalytic Mechanism: Hydrolysis and Transglycosylation Reactions, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6, 421-433 (2010)

5) Sousa, SF; Fernandes, PA; Ramos, MJ, The Search for the Mechanism of the Reaction Catalyzed by Farnesyltransferase, CHEMISTRY-A EUROPEAN JOURNAL,15, 4243-4247 (2009)

6) Munteanu CR; Magalhães AL; Uriarte E; Gonzalez-Diaz H; Multi-target QPDR classification model for human breast and colon cancer-related proteins using star graph topological indices, JOURNAL OF THEORETICAL BIOLOGY, 257(2), 303-311 (2009)

7) Cerqueira, NMFSA; Fernandes PA; Ramos, MJ, MADAMM: a Multi stAged Docking with an Automated Molecular Modelling Protocol, PROTEINS-STRUCTURE, FUNCTION AND BIOINFORMATICS, 74, 192-206 (2009)

8) Dourado, DFAR; Fernandes, PA; ; Mannervik, B; Ramos, MJ, Glutathione Transferase: New model for GSH activation, CHEMISTRY-A EUROPEAN JOURNAL, 14, 9591-9598 (2008)

9) Carvalho, ATP; Swart, M; van Stralen, JNP; Fernandes PA; Ramos MJ; Bickelhaupt FM, Mechanism of thioredoxin-catalyzed disulfide reduction. Activation of the buried thiol and role of the variable active-site residues,  JOURNAL OF PHYSICAL CHEMISTRY B, 112, 2511-2523 (2008)

10) Ramos Maria J.; Fernandes Pedro A., Computational Enzymatic Catalysis, ACCOUNTS OF CHEMICAL RESEARCH, 41, 689-698 (2008)