PDBe-KB: collaboratively defining the biological context of structural data.

Mihály Váradi ,Wim Vranken,Stuart A Mcgowan,Mandar Deshpande,Lennart Martens,Sameer Velankar,Natarajan Kannan,Luis Serrano,Madhusudhan M Srivatsan,Gerardo Pepe,David Armstrong,Karel Berka,Nurul Nadzirin,Paweł Rubach,Nir London,Damiano Piovesan,Jaime Prilusky,Atilio O Rausch,Preeti Choudhary,Franca Fraternali,David Hoksza,Daniel Zaidman,Claudia Andreini,Sucharita Dey,Ahsan Tanweer,Vivek Modi,Valeria Putignano,Natalia Tichshenko,Antonio Rosato,Gulzar Singh,Nathalie Reuter,Alessia David,Manjeet Kumar,Pathmanaban Ramasamy,Jake E Mcgreig,Stephen Anyango,José Marı́a Carazo ,Janet M Thornton ,John M Berrisford ,Thomas A Hopf ,Toby J Gibson ,Carlos Óscar S Sorzano ,Joanna I Sułkowska ,Michael J.e Sternberg ,Lukáš Pravda ,Silvio Tosatto ,Jan Štourač ,Radka Svobodová ,Geoffrey J Barton ,Nathan Rollins ,R Gonzalo Parra ,Emmanuel D Levy ,Bissan Al‐Lazikani ,Mark N Wass ,Tom L Blundell ,Dandan Xue ,Manuela Helmer‐Citterich ,Roland L Dunbrack ,Leandro Radusky ,Dávid Jakubec ,José Ramón Macías ,Juan Fernández Recio ,Christine A Orengo ,Sreenath Nair ,Jiřı́ Damborský ,Kelly Brock ,Radoslav Krivák ,Debora S Marks ,Luis Alejandro Martínez Rodríguez ,Petr Škoda ,David Bednář

doi:10.1093/nar/gkab988

Abstract

The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.

Highlights

The structure of biological macromolecules and their complexes is invaluable for understanding their functions [1,2]
We have added several features, in particular: (i) a superposition service to visualise protein chains clustered by structural similarity; (ii) a bulk download service that provides easy access to all the coordinate files, validation reports, sequences for a protein of interest; (iii) a section dedicated to processed proteins and (iv) annotations for small molecules and macromolecular interaction partners
We described the details of the data process on the public Wiki pages of PDBe-KB at https://github.com/PDBe-KB/ pdbe-kb-manual/wiki/Superposition

Summary

Introduction

The structure of biological macromolecules and their complexes is invaluable for understanding their functions [1,2]. This collaborative consortium aims to place macromolecular structures in their biological context by providing FAIR access to structural, functional and biophysical annotations of protein, nucleic acid and small-molecule structures in the PDB.

Results

Conclusion