The Biofilms Structural Database currently contains atomic information for 501 protein structures, involved in mechanisms of virulence and resistance through biofilm formation and development of 48 organisms, including gram-positive and negative bacteria. All the data is obtained from scientific literature and the Protein Data Bank through data mining. The obtained data is then manually and carefully curated and verified.

Of the 501 entries, 170 are for proteins intervening in the Quorum-sensing network, 62 are proteins involved in Motility mechanisms, 244 are a part of the Extracellular Polymeric Matrix (EPS) and 13 are involved in Dispersion mechanisms.

The information provided for each entry includes category and mechanism of action, organism and respective Gram-type and strain, amino-acid sequence, bound ligands with a biological role in the mechanism, inhibition, mutagenesis, kinetic data, and other spectroscopic and atomic data. A clickable ligand tab directs to a new page, with specific ligand information and an interactive image of its chemical structure. A clickable Protein tab, through its PDB code, directs to specific protein-Ligand interaction information, including a LigPlot obtained interaction map, and a movable image of the protein.

External links to other databases with complementary information are also made available for each entry, namely for ChEMBL, Binding DB, ExPASy, KeGG and UniProt.

Presently, the Biofilms Structural Database contains 188 entries for Pseudomonas aeruginosa, 44 for Escherichia coli , 41 for Staphylococcus aureus, 29 for Clostridioides difficile, 27 for Vibrio cholerae , 21 for Mycobacterium tuberculosis, among others.

The database is easily searchable and exportable. One can export the entire database or manually selected entries in CSV or PDB format.

The Biofilms Structural Database is mantained by the Biomolecular SIMulations Research Group (BioSIM) at Faculdade de Medicina da Universidade do Porto.

This is freely available for both commercial and non-commercial use that can be used online or downloaded in CSV format.

Rita P.Magalhães, Tatiana F.Vieira, Henrique S.Fernandes, André Melo, Manuel Simões, and Sérgio F.Sousa
The Biofilms Structural Database
Trends in Biotechnology (2020)
DOI: 10.1016/j.tibtech.2020.04.002

Download Citation

For questions, feedback and error/bug reports, please contact us at [email protected]