The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.

CEITEC Central European Institute of Technology Masaryk University Brno Kamenice 5 625 00 Brno Bohunice Czech Republic

InterPro European Molecular Biology Laboratory European Bioinformatics Institute Welcome Genome Campus Hinxton Cambridge CB10 1SD UK

Protein Data Bank in Europe European Molecular Biology Laboratory European Bioinformatics Institute Welcome Genome Campus Hinxton Cambridge CB10 1SD UK

Zobrazit více v PubMed

Bernstein F.C., Koetzle T.F., Williams G.J., Meyer E.F., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M.. The Protein Data Bank. Eur. J. Biochem. 1977; 80:319–324. PubMed

Velankar S., Van Ginkel G., Alhroub Y., Battle G.M., Berrisford J.M., Conroy M.J., Dana J.M., Gore S.P., Gutmanas A., Haslam P. et al. . PDBe: Improved accessibility of macromolecular structure data from PDB and EMDB. Nucleic Acids Res. 2016; 44:D385–D395. PubMed PMC

Berman H., Henrick K., Nakamura H.. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 2003; 10:980–980. PubMed

Berman H.M. The Protein Data Bank. Nucleic Acids Res. 2000; 28:235–242. PubMed PMC

Ulrich E.L., Akutsu H., Doreleijers J.F., Harano Y., Ioannidis Y.E., Lin J., Livny M., Mading S., Maziuk D., Miller Z. et al. . BioMagResBank. Nucleic Acids Res. 2008; 36:D402–D408. PubMed PMC

Kinjo A.R., Suzuki H., Yamashita R., Ikegawa Y., Kudou T., Igarashi R., Kengaku Y., Cho H., Standley D.M., Nakagawa A. et al. . Protein Data Bank Japan (PDBj): Maintaining a structural data archive and resource description framework format. Nucleic Acids Res. 2012; 40:D453–D460. PubMed PMC

Young J.Y., Westbrook J.D., Feng Z., Sala R., Peisach E., Oldfield T.J., Sen S., Gutmanas A., Armstrong D.R., Berrisford J.M. et al. . OneDep: unified wwPDB system for deposition, biocuration, and validation of macromolecular structures in the PDB archive. Structure. 2017; 25:536–545. PubMed PMC

Bateman A., Martin M.J., O’Donovan C., Magrane M., Alpi E., Antunes R., Bely B., Bingley M., Bonilla C., Britto R. et al. . UniProt: The universal protein knowledgebase. Nucleic Acids Res. 2017; 45:D158–D169. PubMed PMC

Velankar S., Dana J.M., Jacobsen J., van Ginkel G., Gane P.J., Luo J., Oldfield T.J., O’Donovan C., Martin M.-J., Kleywegt G.J.. SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. Nucleic Acids Res. 2013; 41:D483–D489. PubMed PMC

Fleischmann A., Darsow M., Degtyarenko K., Fleischmann W., Boyce S., Axelsen K.B., Bairoch A., Schomburg D., Tipton K.F., Apweiler R.. IntEnz, the integrated relational enzyme database. Nucleic Acids Res. 2004; 32:D434–D437. PubMed PMC

Blake J.A., Christie K.R., Dolan M.E., Drabkin H.J., Hill D.P., Ni L., Sitnikov D., Burgess S., Buza T., Gresham C. et al. . Gene ontology consortium: Going forward. Nucleic Acids Res. 2015; 43:D1049–D1056. PubMed PMC

Finn R.D., Coggill P., Eberhardt R.Y., Eddy S.R., Mistry J., Mitchell A.L., Potter S.C., Punta M., Qureshi M., Sangrador-Vegas A. et al. . The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016; 44:D279–D285. PubMed PMC

Finn R.D., Attwood T.K., Babbitt P.C., Bateman A., Bork P., Bridge A.J., Chang H.Y., Dosztanyi Z., El-Gebali S., Fraser M. et al. . InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017; 45:D190–D199. PubMed PMC

Murzin A.G., Brenner S.E., Hubbard T., Chothia C.. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 1995; 247:536–540. PubMed

Sillitoe I., Lewis T.E., Cuff A., Das S., Ashford P., Dawson N.L., Furnham N., Laskowski R.A., Lee D., Lees J.G. et al. . CATH: Comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res. 2015; 43:D376–D381. PubMed PMC

Federhen S. The NCBI Taxonomy database. Nucleic Acids Res. 2012; 40:D136–D143. PubMed PMC

Tress M.L., Abascal F., Valencia A.. Alternative splicing may not be the key to proteome complexity. Trends Biochem. Sci. 2017; 42:98–110. PubMed PMC

Suzek B.E., Wang, Huang Y., McGarvey H., Wu P.B., UniProt Consortium C.H.. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics. 2015; 31:926–932. PubMed PMC

Heller S., McNaught A., Stein S., Tchekhovskoi D., Pletnev I.. InChI—the worldwide chemical structure identifier standard. J. Cheminform. 2013; 5:7. PubMed PMC

Law V., Knox C., Djoumbou Y., Jewison T., Guo A.C., Liu Y., MacIejewski A., Arndt D., Wilson M., Neveu V. et al. . DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res. 2014; 42:D1091–D1097. PubMed PMC

Krissinel E., Henrick K.. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 2007; 372:774–797. PubMed

Salavert-Torres J., Iudin A., Lagerstedt I., Sanz-García E., Kleywegt G.J., Patwardhan A.. Web-based volume slicer for 3D electron-microscopy data from EMDB. J. Struct. Biol. 2016; 194:164–170. PubMed PMC

Tagari M., Newman R., Chagoyen M., Carazo J.M., Henrick K.. New electron microscopy database and deposition system. Trends Biochem. Sci. 2002; 27:589. PubMed

Hanson R.M. Jmol-a paradigm shift in crystallographic visualization. J. Appl. Crystallogr. 2010; 43:1250–1260.

Emsley P., Lohkamp B., Scott W.G., Cowtan K.. Features and development of Coot. Acta Crystallogr. Sect. D Biol. Crystallogr. 2010; 66:486–501. PubMed PMC

Waterhouse A.M., Procter J.B., Martin D.M.A., Clamp M., Barton G.J.. Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009; 25:1189–1191. PubMed PMC

Bourne P.E., Berman H.M., McMahon B., Watenpaugh K.D., Westbrook J.D., Fitzgerald P.M.D.. Macromolecular crystallographic information file. Methods Enzymol. 1997; 277:571–590. PubMed

Abriata L.A. Structural database resources for biological macromolecules. Brief. Bioinform. 2017; 18:659–669. PubMed

Yuan S., Chan H.C.S., Hu Z.. Implementing WebGL and HTML5 in macromolecular visualization and modern computer-aided drug design. Trends Biotechnol. 2017; 35:559–571. PubMed

Abriata L.A. Web apps come of age for molecular sciences. Informatics. 2017; 4:28.

Joosten R.P., Salzemann J., Bloch V., Stockinger H., Berglund A.C., Blanchet C., Bongcam-Rudloff E., Combet C., Da Costa A.L., Deleage G. et al. . PDB_REDO: automated re-refinement of X-ray structure models in the PDB. J. Appl. Crystallogr. 2009; 42:376–384. PubMed PMC

Velankar S., Alhroub Y., Best C., Caboche S., Conroy M.J., Dana J.M., Fernandez Montecelo M.A., van Ginkel G., Golovin A., Gore S.P. et al. . PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 2012; 40:D445–D452. PubMed PMC

Velankar S., Kleywegt G.J.. The Protein Data Bank in Europe (PDBe): bringing structure to biology. Acta Crystallogr. D. Biol. Crystallogr. 2011; 67:324–330. PubMed PMC

Levy E.D. PiQSi: Protein Quaternary Structure Investigation. Structure. 2007; 15:1364–1367. PubMed

Gómez J., García L.J., Salazar G.A., Villaveces J., Gore S., García A., Martín M.J., Launay G., Alcántara R., Del-Toro N. et al. . BioJS: an open source JavaScript framework for biological data visualization. Bioinformatics. 2013; 29:1103–1104. PubMed PMC

Valentini E., Kikhney A.G., Previtali G., Jeffries C.M., Svergun D.I.. SASBDB, a repository for biological small-angle scattering data. Nucleic Acids Res. 2015; 43:D357–D363. PubMed PMC

Iudin A., Korir P.K., Salavert-Torres J., Kleywegt G.J., Patwardhan A.. EMPIAR: a public archive for raw electron microscopy image data. Nat. Methods. 2016; 13:387–388. PubMed

Morin A., Eisenbraun B., Key J., Sanschagrin P.C., Timony M.A., Ottaviano M., Sliz P.. Collaboration gets the most out of software. Elife. 2013; 2:e01456. PubMed PMC

Grabowski M., Langner K.M., Cymborowski M., Porebski P.J., Sroka P., Zheng H., Cooper D.R., Zimmerman M.D., Elsliger M.A., Burley S.K. et al. . A public database of macromolecular diffraction experiments. Acta Crystallogr. Sect. D Struct. Biol. 2016; 72:1181–1193. PubMed PMC

Bento A.P., Gaulton A., Hersey A., Bellis L.J., Chambers J., Davies M., Krüger F.A., Light Y., Mak L., McGlinchey S. et al. . The ChEMBL bioactivity database: an update. Nucleic Acids Res. 2014; 42:D1083–D1090. PubMed PMC

Golovin A., Henrick K.. MSDmotif: exploring protein sites and motifs. BMC Bioinformatics. 2008; 9:312. PubMed PMC

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

PDBe: improved findability of macromolecular structure data in the PDB

An intrinsically disordered proteins community for ELIXIR

3DPatch: fast 3D structure visualization with residue conservation

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)

Worldwide Protein Data Bank validation information: usage and trends

Validation of ligands in macromolecular structures determined by X-ray crystallography