Biology subjects

Berrisford, J.

Publications and source records attributed to Berrisford, J..

3 recordsLinked to original sources

bioRxiv2023

PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank

The Protein Data Bank (PDB) archive is the global repository for public-domain 3D biomolecular structural information. The archival nature of the PDB presents certain challenges pertaining to updating or adding associated annotations from trusted external biodata resources. While each Worldwide PDB (wwPDB) partner has made best efforts to provide up-to-date external annotations, accessing and integrating information from disparate wwPDB data centers can be an involved process. To address this issue, the wwPDB has established the PDB Next Generation or NextGen Archive, developed to centralize and streamline access to enriched structural annotations from wwPDB partners and trusted external sources. At present, the archive provides mappings between experimentally determined 3D structures of proteins and UniProt amino acid sequences, together with domain annotations from Pfam, SCOP2, and CATH databases, and intra-molecular connectivity information. Since launch, the PDB NextGen Archive has seen substantial user engagement with over 3.5 million data file downloads, ensuring researchers have access to accurate, up-to-date, and easily accessible structural annotations. Database URLhttp://www.wwpdb.org/ftp/pdb-nextgen-archive-site

bioinformatics↗

bioRxiv2023

Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data

Macromolecular complexes are essential functional units in nearly all cellular processes, and their atomic-level understanding is critical for elucidating and modulating molecular mechanisms. The Protein Data Bank (PDB) serves as the global repository for experimentally determined structures of macromolecules. Structural data in the PDB offer valuable insights into the dynamics, conformation, and functional states of biological assemblies. However, the current annotation practices lack standardised naming conventions for assemblies in the PDB, complicating the identification of instances representing the same assembly. In this study, we introduce a method leveraging resources external to PDB, such as the Complex Portal, UniProt and Gene Ontology, to describe assemblies and contextualise them within their biological settings accurately. Employing the proposed approach, we assigned standard names and provided value-added annotations to over 90% of unique assemblies in the PDB. This standardisation of assembly data enhances the PDB, facilitating a deeper understanding of these cellular components. Furthermore, the data standardisation improves the PDBs FAIR attributes, fostering more effective basic and translational research and education across scientific disciplines.

bioinformatics↗

bioRxiv2022

Unified access to up-to-date residue-level annotations from UniProt and other biological databases for PDB data via PDBx/mmCIF files

More than 58,000 proteins have up-to-date correspondence between their amino acid sequence (UniProtKB) and their 3D structures (PDB), enabled by the Structure Integration with Function, Taxonomy and Sequences (SIFTS) resource. In addition to this fundamental mapping, SIFTS incorporates residue-level annotations from other biological resources such as Pfam, InterPro, SCOP, SCOP2, CATH, IntEnz, GO, PubMed, Ensembl, NCBI taxonomy database and Homologene. The SIFTS data is exported in XML format per individual PDB entry and is also accessible via the PDBe REST API. These mappings have always been maintained separately from the structure data (PDBx/mmCIF file) in the PDB archive. In this current work, taking advantage of the extensibility of the core PDBx/mmCIF framework, we extended the wwPDB PDBx/mmCIF data dictionary with additional categories to accommodate SIFTS data and added the UniProt, Pfam, SCOP2, and CATH mapping information directly into the PDBx/mmCIF files from the PDB archive. The integration of mapping data in the PDBx/mmCIF files provides consistent numbering of residues in different PDB entries allowing easy comparison of structure models. The extended PDBx/mmCIF format yields a more consistent, standardised metadata description without altering the core PDB information. This development enables up-to-date cross-reference information at residue level resulting in better data interoperability, supporting improved data analysis and visualisation. Availability and implementationWe expanded the PDBe release pipeline with a process that adds SIFTS annotations to the PDBx/mmCIF files for individual structures in the PDB archive. The scientific community can download these updated PDBx/mmCIF files from the PDBe entry pages (https://pdbe.org/7dr0) and through direct URLs (https://www.ebi.ac.uk/pdbe/static/entry/7o9f_updated.cif), using the PDBe download service (https://www.ebi.ac.uk/pdbe/download/api) or from the EMBL-EBI FTP area (https://ftp.ebi.ac.uk/pub/databases/msd/updated_mmcif/).

bioinformatics↗