Research Lab

BioMolecular Simulations

biosim
56737

Lab Members

Lab leader

Nuno Manuel Ferreira de Sousa de Azevedo Cerqueira
Sergio Filipe Maia de Sousa

Independent researcher

Pedro J Silva

PhD students

André Pina
Andreia D. Veloso
Carla Sílvia Silva Teixeira
Cátia Santos-Pereira
Henrique Fernandes
Juliana Rocha
Olívia Pontes
Rita P. Magalhães
Susana Fernandes
Tatiana Vieira

Other members

Fábio António Gouveia Ferreria Martins
Research Interests

Our research topics include Computational Enzymatic Catalysis, Computational Drug Discovery and the Study of Molecular Recognition in Biological Systems. For that we combine QM/MM Methods, Quantum Mechanics, Molecular Dynamics, Docking, Virtual Screening, and Free Energy Perturbation methods, always in close linking with experiment.

 

Our lab is also involved in the development of software applications and scientific databases.

Research Highlights
Tailoring Computational Tools for Enzymatic Catalysis, Biomolecular Recognition and Drug Discovery

 

The Biofilms Structural Database (BSD) is a database of reference for the study of biofilm inhibition developed and maintained at UCIBIO@BioSIM. It is a curated collection of structural, mutagenesis, kinetics, and inhibition data focusing on biofilm inhibition for 42 different bacteria available at www.biofilms.biosim.pt.


Tryptophan Synthase (TSase) is an emergent target for the treatment of tuberculosis. We have used QM/MM calculations to analyze  and explain the catalytic mechanism of this enzyme. The results provide an atomic-level clarification of its full catalytic mechanism offering important clues for the rational development of new inhibitors against tuberculosis.

 

highlight 2020

Selected Publications

Lapaillerie, D; Charlier, C; Fernandes, HS; Sousa, SF; Lesbats, P; Weigel, P; Favereaux, A; Guyonnet-Duperat, V; Parissi, V. 2021. In Silico, In Vitro and In Cellulo Models for Monitoring SARS-CoV-2 Spike/Human ACE2 Complex, Viral Entry and Cell Fusion. Viruses-Basel, 13, DOI: 10.3390/v13030365
Ribeiro, PMG; Fernandes, HS; Maia, LB; Sousa, SF; Moura, JJG; Cerqueira, NMFSA. 2021. The complete catalytic mechanism of xanthine oxidase: a computational study. Inorganic Chemistry Frontiers, 8, DOI: 10.1039/d0qi01029d
Gonçalves, IG; Fernandes, HS; Melo, A; Sousa, SF; Simões, LC; Simões, M. 2021. LegionellaDB – A Database on Legionella Outbreaks. TRENDS IN MICROBIOLOGY, DOI: 10.1016/j.tim.2021.01.015
Rita PMagalhães; Tatiana FVieira; Henrique SFernandes; André Melo; Manuel Simões; Sérgio FSousa. 2020. The Biofilms Structural Database. TRENDS IN BIOTECHNOLOGY, 38(9), DOI: 10.1016/j.tibtech.2020.04.002