Theoretical and Computational Biosciences

Theoretical and Computational Biochemistry

The TCB Group develops research in computational and theoretical sciences and is focused on 4 main lines of research - enzymatic catalysis, drug discovery, nanotechnology and crude oil desulfurization.

Our success in unraveling enzymatic mechanisms has granted us the recognition of the international scientific community and we have been invited to numerous plenary talks. In an effort to bridge fundamental and applied research, the group is also collaborating with several major companies in drug development, such as Bial, in order to develop different inhibitors for different enzymes. We have devised a protocol for drug discovery, which is granting us with major successes in the area of designing drugs.

Regarding projects with environmental impact, we are improving/accelerating the process of crude oil desulfurization, making it cleaner and less expensive, through the use of new, tailor-made enzymatic biocatalysts. Theoretical models have been developed to correlate amino acid sequence patterns with the formation of alpha-helix motifs and protein function. In parallel we conducted reactivity studies of chemical molecules that are important in biological processes.
The innovative approaches used to address these topics are internationally recognized and are the basis of several pieces of software used world-wide, as VMD (Visual Molecular Dynamics) plug-ins. These plug-ins are related to molecular docking, virtual screening and computational mutagenesis, all of them invaluable methodologies in Drug Discovery.

In 2013-2017 the TCB group has published 151 papers in WoS journals with 992 citations as well as 4 books/book chapters, 4 computer softwares with novel algorithms; supervised 15 PhD and 13 MSc theses; participated in 1 international project and 15 national projects (9 as PI), with an approximate total funding of 1.1M€.

TCB Research Labs
Recent publications
Prudêncio P, Rebelo K, Grosso AR, Martinho RG, Carmo-Fonseca M.. 2019. Analysis of Mammalian Native Elongating Transcript sequencing (mNET-seq) high-throughput data. METHODS, DOI: 10.1016/j.ymeth.2019.09.003
Mafalda Ramos de Matos; Ioana Posa; Filipa Sofia Carvalho; Vanessa Alexandra Morais; Ana Rita Grosso; Sérgio Fernandes de Almeida. 2019. A Systematic Pan-Cancer Analysis of Genetic Heterogeneity Reveals Associations with Epigenetic Modifiers. Cancers, DOI: 10.3390/cancers11030391
Listyarini, RV; Gesto, DS; Paiva, P; Ramos, MJ; Fernandes, PA. 2019. Benchmark of Density Functionals for the Calculation of the Redox Potential of Fe3+/Fe2+ Within Protein Coordination Shells. Frontiers in Chemistry, 7, DOI: 10.3389/fchem.2019.00391
Moreira, CDD; Ramos, MJRN; Fernandes, PMAA. 2019. Glutamine synthetase structure-catalysis relationship-Recent advances and applications. Wiley Interdisciplinary Reviews-Computational Molecular Science, 9, DOI: 10.1002/wcms.1399
Alexandra CVítor; Sreerama CSridhara; João CSabino; Ana IAfonso; Ana RGrosso; Robert MMartin; Sérgio Fde Almeida. 2019. Single-molecule imaging of transcription at damaged chromatin. Science Advances, 5(1), DOI: 10.1126/sciadv.aau1249