The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank in Europe (PDBe; pdbe.org) team develops and maintains several databases and web services to address this fundamental need. From data archiving as a member of the Worldwide PDB consortium (wwPDB; wwpdb.org), to the PDBe Knowledge Base (PDBe-KB; pdbekb.org), we provide data, data-access mechanisms, and visualizations that facilitate basic and applied research and education across the life sciences. Here, we provide an overview of the structural data and annotations that we integrate and make freely available. We describe the web services and data visualization tools we offer, and provide information on how to effectively use or even further develop them. Finally, we discuss the direction of our data services, and how we aim to tackle new challenges that arise from the recent, unprecedented advances in the field of structure determination and protein structure modeling.

CEITEC Central European Institute of Technology Masaryk University Brno Czech Republic

European Molecular Biology Laboratory European Bioinformatics Institute Hinxton

National Centre for Biomolecular Research Faculty of Science Masaryk University Brno Czech Republic

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wwPDB consortium , Burley SK, Berman HM, et al. Protein Data Bank: The single global archive for 3D macromolecular structure data. Nucleic Acids Res. 2019;47:D520–D528. PubMed PMC

Armstrong DR, Berrisford JM, Conroy MJ, et al. PDBe: Improved findability of macromolecular structure data in the PDB. Nucleic Acids Res. 2019;48(D1):D335–D343. PubMed PMC

Rose Y, Duarte JM, Lowe R, et al. RCSB Protein Data Bank: architectural advances towards integrated searching and efficient access to macromolecular structure data from the PDB archive. J Mol Biol. 2021;433:166704. PubMed PMC

Kinjo AR, Bekker G‐J, Suzuki H, et al. Protein Data Bank Japan (PDBj): Updated user interfaces, resource description framework, analysis tools for large structures. Nucleic Acids Res. 2017;45:D282–D288. PubMed PMC

Romero PR, Kobayashi N, Wedell JR, et al. BioMagResBank (BMRB) as a resource for structural biology. Methods Mol Biol. 2020;2112:187–218. PubMed PMC

Abbott S, Iudin A, Korir PK, Somasundharam S, Patwardhan A. EMDB web resources. Curr Protoc Bioinformatics. 2018;61:5.10.1–5.10.12. PubMed PMC

Burley SK, Berman HM, Christie C, et al. RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. Protein Sci Publ Protein Soc. 2018;27:316–330. PubMed PMC

Jumper J, Evans R, Pritzel A, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596:583–589. PubMed PMC

Baek M, DiMaio F, Anishchenko I, et al. Accurate prediction of protein structures and interactions using a three‐track neural network. Science. 2021;373:871–876. PubMed PMC

Gerstein M. Integrative database analysis in structural genomics. Nat Struct Biol. 2000;7(Suppl):960–963. PubMed

PDBe‐KB consortium . PDBe‐KB: Collaboratively defining the biological context of structural data. Nucleic Acids Res. 2022;50:D534–D542. PubMed PMC

Mitsopoulos C, Di Micco P, Fernandez EV, et al. canSAR: Update to the cancer translational research and drug discovery knowledgebase. Nucleic Acids Res. 2021;49:D1074–D1082. PubMed PMC

Cilia E, Pancsa R, Tompa P, Lenaerts T, Vranken WF. The DynaMine webserver: Predicting protein dynamics from sequence. Nucleic Acids Res. 2014;42:W264–W270. PubMed PMC

Wass MN, Kelley LA, Sternberg MJE. 3DLigandSite: Predicting ligand‐binding sites using similar structures. Nucleic Acids Res. 2010;38:W469–W473. PubMed PMC

Pravda L, Sehnal D, Svobodová Vařeková R, et al. ChannelsDB: Database of biomacromolecular tunnels and pores. Nucleic Acids Res. 2018;46:D399–D405. PubMed PMC

Wilkinson MD, Dumontier M, Aalbersberg IJJ, et al. The FAIR guiding principles for scientific data management and stewardship. Sci Data. 2016;3:160018. PubMed PMC

Orengo C, Velankar S, Wodak S, et al. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D‐Bioinfo Community). F1000Research. 2020;9:278. PubMed PMC

Nair S, Váradi M, Nadzirin N, et al. PDBe aggregated API: Programmatic access to an integrative knowledge graph of molecular structure data Gorodkin J, editor. Bioinformatics. 2021;37(21):3950–3952. PubMed PMC

PDBe‐KB consortium , Varadi M, Berrisford J, et al. PDBe‐KB: A community‐driven resource for structural and functional annotations. Nucleic Acids Res. 2020;48:D344–D353. PubMed PMC

Varadi M, Anyango S, Deshpande M, et al. AlphaFold protein structure database: Massively expanding the structural coverage of protein‐sequence space with high‐accuracy models. Nucleic Acids Res. 2022;50:D439–D444. PubMed PMC

Sehnal D, Bittrich S, Deshpande M, et al. Mol* Viewer: Modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res. 2021;49:W431–W437. PubMed PMC

Deshpande M, Varadi M, Paysan‐Lafosse T, et al. PDB ProtVista: A reusable and open‐source sequence feature viewer. BioRxiv. 2022.

Dana JM, Gutmanas A, Tyagi N, et al. SIFTS: Updated structure integration with function, taxonomy and sequences resource allows 40‐fold increase in coverage of structure‐based annotations for proteins. Nucleic Acids Res. 2019;47:D482–D489. PubMed PMC

Young JY, Westbrook JD, Feng Z, et al. (2017) OneDep: Unified wwPDB system for deposition, biocuration, and validation of macromolecular structures in the PDB archive. Struct Lond Engl. 1993;25:536–545. PubMed PMC

Khanna T, Hanna G, Sternberg MJE, David A. Missense3D‐DB web catalogue: An atom‐based analysis and repository of 4M human protein‐coding genetic variants. Hum Genet. 2021;140:805–812. PubMed PMC

Delgado J, Radusky LG, Cianferoni D, Serrano L. FoldX 5.0: Working with RNA, small molecules and a new graphical interface Valencia A, editor. Bioinformatics. 2019;35:4168–4169. PubMed PMC

Blum M, Chang H‐Y, Chuguransky S, et al. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 2021;49:D344–D354. PubMed PMC

Sillitoe I, Dawson N, Lewis TE, et al. CATH: Expanding the horizons of structure‐based functional annotations for genome sequences. Nucleic Acids Res. 2019;47:D280–D284. PubMed PMC

Mistry J, Chuguransky S, Williams L, et al. Pfam: The protein families database in 2021. Nucleic Acids Res. 2021;49:D412–D419. PubMed PMC

Cunningham F, Allen JE, Allen J, et al. Ensembl 2022. Nucleic Acids Res. 2022;50:D988–D995. PubMed PMC

Andreeva A, Kulesha E, Gough J, Murzin AG. The SCOP database in 2020: Expanded classification of representative family and superfamily domains of known protein structures. Nucleic Acids Res. 2020;48:D376–D382. PubMed PMC

Feolo M, Helmberg W, Sherry S, Maglott DR. NCBI genetic resources supporting immunogenetic research. Rev Immunogenet. 2000;2:461–467. PubMed

UniProt Consortium . UniProt: The universal protein knowledgebase in 2021. Nucleic Acids Res. 2021;49:D480–D489. PubMed PMC

Stelzer G, Rosen N, Plaschkes I, et al. The GeneCards suite: From gene data mining to disease genome sequence analyses. Curr Protoc Bioinforma. 2016;54:1.30.1–1.30.33. PubMed

Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM. PDBsum: Structural summaries of PDB entries. Protein Sci Publ Protein Soc. 2018;27:129–134. PubMed PMC

Sweeney BA, Hoksza D, Nawrocki EP, et al. R2DT is a framework for predicting and visualising RNA secondary structure using templates. Nat Commun. 2021;12:3494. PubMed PMC

Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB. FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol. 2008;56:215–252. PubMed PMC

Mukhopadhyay A, Borkakoti N, Pravda L, Tyzack JD, Thornton JM, Velankar S. Finding enzyme cofactors in Protein Data Bank Wren J, editor. Bioinformatics. 2019;35:3510–3511. PubMed PMC

Kleinjung J, Fraternali F. POPSCOMP: An automated interaction analysis of biomolecular complexes. Nucleic Acids Res. 2005;33:W342–W346. PubMed PMC

Tiwari SP, Fuglebakk E, Hollup SM, et al. WEBnm@ v2.0: Web server and services for comparing protein flexibility. BMC Bioinformatics. 2014;15(427):427. PubMed PMC

Fontana P, Dong Y, Pi X, et al. Structure of cytoplasmic ring of nuclear pore complex by integrative cryo‐EM and AlphaFold. Science. 2022;376:eabm9326. PubMed PMC

Mosalaganti S, Obarska‐Kosinska A, Siggel M, et al. AI‐based structure prediction empowers integrative structural analysis of human nuclear pores. Science. 2022;376:eabm9506. PubMed

Tian R, Li Y, Wang X, et al. A pharmacoinformatics analysis of artemisinin targets and de novo design of hits for treating ulcerative colitis. Front Pharmacol. 2022;13:843043. PubMed PMC

Binder JL, Berendzen J, Stevens AO, et al. AlphaFold illuminates half of the dark human proteins. Curr Opin Struct Biol. 2022;74:102372. PubMed PMC

Cai SW, Zinder JC, Svetlov V, et al. Cryo‐EM structure of the human CST‐Polα/primase complex in a recruitment state. Nat Struct Mol Biol. 2022;29(8):813–819. PubMed PMC

Collar AL, Linville AC, Core SB, Frietze KM. Epitope‐based vaccines against the chlamydia trachomatis major outer membrane protein variable domain 4 elicit protection in mice. Vaccine. 2022;10:875. PubMed PMC

Wehrspan ZJ, McDonnell RT, Elcock AH. Identification of iron‐sulfur (Fe‐S) cluster and zinc (Zn) binding sites within proteomes predicted by DeepMind's AlphaFold2 program dramatically expands the metalloproteome. J Mol Biol. 2022;434:167377. PubMed PMC

Bludau I, Willems S, Zeng W‐F, et al. The structural context of posttranslational modifications at a proteome‐wide scale. PLoS Biol. 2022;20:e3001636. PubMed PMC

Mesoscale explorer: Visual exploration of large-scale molecular models

Mesoscale Explorer - Visual Exploration of Large-Scale Molecular Models

Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit

αCharges: partial atomic charges for AlphaFold structures in high quality