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Biomolecular Simulation Laboratory

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Biomolecular Simulation Laboratory


About the BSL

The Biomolecular Simulation Laboratory (BSLab) both develops and applies computational molecular modelling and structural bioinformatics methodologies to the study of structure and function of biological macromolecules.  Applications studies   include the molecular details of the oxidative protein folding pathways in the ER, the structure-function relationships in polymorphic variants of CYP drug-metabolizing enzymes, and molecular mechanisms of adaption to cold environments. Methodological studies included  the development of  new sfotware and methods for macromolecular electrostatics calculations and application of computer graphjcs and Virtual Reality to molecular modelling and visualization.


Select Publications (2008-2017)

Gouveia, P. and Martel, P.,(2017), “Player Experience, Gaming and VR Technologies (extended version)”. Revista de Ciências da Computação, Universidade Aberta. Edição Especial Videojogos 2016.

Marques C.L., Fernández I., Viegas M.N., Cox C.J., Martel P., Rosa J., Cancela M.L., Laizé V. (2016) “Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: molecular and evolutionary perspectives.”  Cell. Mol Life Sci. 73(4):841-57.

Silva, G., Lima F.P., Martel P., Castilho R. (2014) “Thermal adaptation and clinal mitochondrial DNA variation of European anchovy”. Proc. R. Soc. B 281:20141093.

Varanda C.M., Machado M., Martel P., Nolasco G., Clara M.I, Félix M.R. (2014) “Genetic diversity of the coat protein of Olive mild mosaic virus (OMMV) and Tobacco necrosis virus D (TNV-D) isolates and its structural implications”. PLoS One 9(10):e110941.

Martel P (2014). “A Curiosidade Cura: Importância da Investigação Básica em Biomedicina” Cidade Solidária (Revista da Santa Casa da Misericórdia de Lisboa), 31:1921.

Freedman H., Martel P., Cruzeiro L. (2010) “Mixed quantum-classical dynamics of an amide-l vibrational excitation in a protein alpha-helix”. Phys. Rev. B, 82(17):174308

Texeira V.H., Ribeiro, V., Martel P.J. (2010) “Analysis of Binding Modes of Ligands to Multiple Conformations of CYP3A4”, Biochim Biophys Acta, 1804:2036-2045.


Project Grants

POCTI/BME/34701/99 “Structure and function of elicitins and their role in the infection of the cork oak by Phytophthora cinnamomi”.

Collaborator/ team member

PTDC/QUI-BIQ/119677/2010 “A Biophysical Approach to Oxidative Protein Folding in the ER: Relative Importance of Ero1 and Prdx4 alternative pathways”, 2012-2014.

PTDC/QUI/72631/2006 “Thermodynamic Signature of the Pregnane Xenobiotic Receptor Activation by Quartz Crystal Microbalance with Heat Conduction Calorimetry”, 2009-2011.

POCTI/BIO/62476/2004 “Viral Nanoparticles for molecular and gene therapy”, 2009-2011.

POCI/QUI/63166/2004 “Theoretical and experimental studies of enzyme conformation, energetics and dynamics of CYP3A4.”

POCTI/MGI/48417/2002 “Relationship between CYP3A4 gene polymorphism, protein structure and activity in disease setting”.


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