Research Lab

BioMolecular Simulations

biosim
56737
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

Juliana FRocha; Sérgio FSousa; Nuno MFSousa ACerqueira. 2022. Computational Studies Devoted to the Catalytic Mechanism of Threonine Aldolase, a Critical Enzyme in the Pharmaceutical Industry to Synthesize β-Hydroxy-α-amino Acids. ACS Catalysis, DOI: 10.1021/acscatal.1c05567
Juliana FRocha; Sérgio FSousa; Nuno MFSousa ACerqueira. 2022. Computational Studies Devoted to the Catalytic Mechanism of Threonine Aldolase, a Critical Enzyme in the Pharmaceutical Industry to Synthesize β-Hydroxy-α-amino Acids. ACS Catalysis, DOI: 10.1021/acscatal.1c05567
Juliana FRocha; Sérgio FSousa; Nuno MFSousa ACerqueira. 2022. Computational Studies Devoted to the Catalytic Mechanism of Threonine Aldolase, a Critical Enzyme in the Pharmaceutical Industry to Synthesize β-Hydroxy-α-amino Acids. ACS Catalysis, DOI: 10.1021/acscatal.1c05567
Rita PMagalhães; Henrique SFernandes; Sérgio FSousa. 2022. The critical role of Asp206 stabilizing residues on the catalytic mechanism of the Ideonella sakaiensis PETase. Catalysis Science & Technology, DOI: 10.1039/D1CY02271G
Rita PMagalhães; Henrique SFernandes; Sérgio FSousa. 2022. The critical role of Asp206 stabilizing residues on the catalytic mechanism of the Ideonella sakaiensis PETase. Catalysis Science & Technology, DOI: 10.1039/D1CY02271G