In our lab, we are integrated into multidisciplinary projects centered on two major themes (data science and structural modeling) for which we established a network of international and national collaborations, both experimental and theoretical. In fact, we lead teams of geographically distributed researchers with very diverse scientific backgrounds to work at the interface of Computer Science and Structural Biology. We have extensive expertise in using data from the literature as well as cutting-edge high-throughput technologies combined with computational/mathematical approaches to study biological systems and network architectures of complex diseases. This knowledge is all integrated to develop new and more targeted therapies. 

Keywords

Bioinformatics

Computational Biology

Data Science

Machine Learning

Structural Modeling 

Research Lines 

1 - Data Science

Contrary to the reductionist approach aimed at understanding individual components, the new data revolution allows the understanding of complicated interactions and pathways through the use of statistical Data Mining/Machine-Learning (ML) techniques. These are active areas of research in computer science with the increasing availability of big data collections of all sorts prompting interest in the development of novel tools for data mining. It is expected that continuous improvement of software infrastructure will make ML applicable to a growing range of biological problems. We envision, plan, and manage large and completely independent projects that merged knowledge from chemistry, bioinformatics, biophysics, statistics, and data-mining to build innovative and completely new methods and computational solutions. Striking examples are the application of ML to:

Ongoing Research Projects 

Selected Publications 

Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue LC, Honorato RV, Moreira IS, Kurkcuoglu Z, Vangone A, Bonvin AMJJ, An overview of data-driven HADDOCK stratergies in CAPRI rounds 38-45, Proteins, 2020, https://doi.org/10.1002/prot.25869

Matos-Filipe P, Preto AJ, Koukos PI, Mourao J, Bonvin AMJJ, Moreira IS, MENSADB: a through structural analysis of membrane protein dimers, 2019, arXiv: 1999; 1902.02321.