Database

The DSB hosts the UNIPD node of ELIXIR, the European Research Infrastructure for life-science data. ELIXIR is dedicated to providing the scientific community with a state-of-the-art infrastructure for Bioinformatics, featuring advanced platforms and services for the analysis of genomic, proteomic, and metabolomic data.
DSB hosts several databases, registries, tools and predictors which are included in the ELIXIR service delivery plan (SDP) of the national ELIXIR node. A number of resources maintained and developed at DSB are globally recognized to be central in the context of structural biology and especially for what regards the field of intrinsically disordered proteins (IDPs).

MobiDB
MobiDB is a unique resource that serves as a comprehensive knowledgebase of intrinsically disordered proteins and regions that was first published in 2012 with the aim of providing a comprehensive overview of the functional role of disordered regions in proteins. MobiDB strives to generate new knowledge and capture the functional significance of disordered regions by processing and combining complementary sources of information. It aggregates disorder annotations from the literature and experimental evidence, along with predictions, for all known protein sequences. Curated data from literature evidence is directly pulled from third-party resources, building on extensive and fruitful collaborations with many databases and consortia. MobiDB predictions are integrated into UniProtKB, InterPro, PDBe among other databases.

DisProt
DisProt provides manually curated annotations of intrinsically disordered proteins from the literature. Whereas predicted disorder features are available in MobiDB the crux of understanding protein disorder is the availability of manually curated, experimentally verified disorder annotations. Compared with MobiDB which aggregate data and expand the annotation leveraging reliable predictions, DisProt provides detailed information about the experimental conditions through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia. DisProt provides the ground truth of the Critical Assessment of protein Intrinsic Disorder (CAID) initiative for an unbiased evaluation of disorder predictors, including the evaluation of the AlphaFold method.

PED
The Protein Ensemble Database (PED) is the primary resource for depositing structural ensembles of intrinsically disordered proteins. The main goal of PED is to provide an ever-growing platform of structural ensemble entries with a user-friendly deposition pipeline while maintaining high standards for data quality and the FAIR data principles. PED is cross-linked with the main resources to deposit ensembles’ primary experimental data, including BRMB, SASBDB and PCDDB. PED ensembles are predominantly modelled using SAXS, NMR spectroscopy, FRET data and their combinations. NMR data included chemical shifts (CSs), nuclear Overhauser effects (NOEs), J-couplings, residual dipolar couplings (RDCs), relaxation data and paramagnetic relaxation enhancements (PREs). PED is part of the 3D-Beacons network.

APICURON
APICURON is a platform designed to credit and acknowledge scientific contributions, with a focus on tracking biocuration events to ensure appropriate credit and visibility for researchers. It provides recognition for contributions to scientific artifacts beyond traditional publications, including research data, software, tools, workflows, and training. By partnering with platforms like ORCID and BIP! Scholar, APICURON ensures that scientists receive appropriate credit for their contributions while promoting sustainable practices in research.

DOME Registry
The DOME Registry is a database designed to manage and access comprehensive information related to the validation and reproducibility of machine learning based studies. Built around the DOME recommendations, this registry facilitates standardization in the evaluation of ML methods.