EMDB-the Electron Microscopy Data Bank.

wwPDB Consortium .

Nucleic Acids Res, 2024

doi:10.1093/nar/gkad1019.

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

Appasamy SD, Berrisford J, Gaborova R, Nair S, Anyango S, Grudinin S, Deshpande M, Armstrong D, Pidruchna I, Ellaway JIJ, Leines GD, Gupta D, Harrus D, Varadi M, Velankar S.

Sci Data, 2023

doi:10.1038/s41597-023-02778-9.

PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education.

Varadi M, Anyango S, Appasamy SD, Armstrong D, Bage M, Berrisford J, Choudhary P, Bertoni D, Deshpande M, Leines GD, Ellaway J, Evans G, Gaborova R, Gupta D, Gutmanas A, Harrus D, Kleywegt GJ, Bueno WM, Nadzirin N, Nair S, Pravda L, Afonso MQL, Sehnal D, Tanweer A, Tolchard J, Abrams C, Dunlop R, Velankar S.

Protein Sci, 2022

doi:10.1002/pro.4439.

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

PDBe-KB consortium.

Nucleic Acids Res, 2022

doi:10.1093/nar/gkab988.

A guide to analysing binding sites in protein structures

Armstrong D.

2021

doi:10.6019/tol.bindingsites-w.2021.00001.1.

PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data.

Nair S, Váradi M, Nadzirin N, Pravda L, Anyango S, Mir S, Berrisford J, Armstrong D, Gutmanas A, Velankar S.

Bioinformatics, 2021

doi:10.1093/bioinformatics/btab424.

PDBe: improved findability of macromolecular structure data in the PDB.

Armstrong DR, Berrisford JM, Conroy MJ, Gutmanas A, Anyango S, Choudhary P, Clark AR, Dana JM, Deshpande M, Dunlop R, Gane P, Gáborová R, Gupta D, Haslam P, Koča J, Mak L, Mir S, Mukhopadhyay A, Nadzirin N, Nair S, Paysan-Lafosse T, Pravda L, Sehnal D, Salih O, Smart O, Tolchard J, Varadi M, Svobodova-Vařeková R, Zaki H, Kleywegt GJ, Velankar S.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkz990.

PDBe-KB: a community-driven resource for structural and functional annotations.

PDBe-KB consortium.

Nucleic Acids Res, 2020

doi:10.1093/nar/gkz853.

Protein Structure Databases

Armstrong DA, Berrisford JM, Conroy MJ, Clark AR, Gupta D, Mukhopadhyay A.

2019

doi:10.1016/b978-0-12-809633-8.20280-x.

Protein Data Bank: the single global archive for 3D macromolecular structure data.

wwPDB consortium.

Nucleic Acids Res, 2019

doi:10.1093/nar/gky949.

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

Young JY, Westbrook JD, Feng Z, Peisach E, Persikova I, Sala R, Sen S, Berrisford JM, Swaminathan GJ, Oldfield TJ, Gutmanas A, Igarashi R, Armstrong DR, Baskaran K, Chen L, Chen M, Clark AR, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Ikegawa Y, Kengaku Y, Lawson CL, Liang Y, Mak L, Mukhopadhyay A, Narayanan B, Nishiyama K, Patwardhan A, Sahni G, Sanz-García E, Sato J, Sekharan MR, Shao C, Smart OS, Tan L, van Ginkel G, Yang H, Zhuravleva MA, Markley JL, Nakamura H, Kurisu G, Kleywegt GJ, Velankar S, Berman HM, Burley SK.

Database (Oxford), 2018

doi:10.1093/database/bay002.

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.

Mir S, Alhroub Y, Anyango S, Armstrong DR, Berrisford JM, Clark AR, Conroy MJ, Dana JM, Deshpande M, Gupta D, Gutmanas A, Haslam P, Mak L, Mukhopadhyay A, Nadzirin N, Paysan-Lafosse T, Sehnal D, Sen S, Smart OS, Varadi M, Kleywegt GJ, Velankar S.

Nucleic Acids Res, 2018

doi:10.1093/nar/gkx1070.

Human genetic variation (II): exploring publicly available data

Armstrong D, Burke M, Emery L, MacArthur J, Nightingale A, Perry E, Pundir S, Saunders G.

2017

doi:10.6019/tol.hugenvar_2-t.2017.00001.1.

Human genetic variation (I): an introduction

Armstrong D, Burke M, Emery L, MacArthur J, Nightingale A, Perry E, Pundir S, Saunders G.

2017

doi:10.6019/tol.hugenvar_1-t.2017.00001.1.

10th Anniversary Treasure Hunt

Armstrong D, Burke M, Huerta L, Levchenko M, Mitchell A, Morgan S, Mugumbate G, Mutowo P, Orchard S, Perry E, Pundir S, Richardson L, Tang A.

2017

doi:10.6019/tol.treasure-t.2017.00001.1.

EMBL-EBI, programmatically: take a REST from manual searches

Burke M, Armstrong D, Carvalho-Silva D, Castro L, Cowley A, Finn R, Foix A, Katuri J, Laird M, Lee J, Levchenko M, Lopez R, Nightingale A, Nightingale A, Nowotka M, Perry E, Pichler K, Pundir S, Morgan S, Saunders G, Garcia P, Squizzato S.

2017

doi:10.6019/tol.ebiprogrammatically-w.2017.00001.1.

Visualising protein structures online

Armstrong A.

2017

doi:10.6019/tol.pdbe-litemol-w.2017.00001.1.

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK.

Structure, 2017

doi:10.1016/j.str.2017.01.004.

Synthesis of Chlorophyll-Binding Proteins in a Fully Segregated Δycf54 Strain of the Cyanobacterium Synechocystis PCC 6803.

Hollingshead S, Kopečná J, Armstrong DR, Bučinská L, Jackson PJ, Chen GE, Dickman MJ, Williamson MP, Sobotka R, Hunter CN.

Front Plant Sci, 2016

doi:10.3389/fpls.2016.00292.

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Lagerstedt I, Mir S, Fernandez Montecelo MA, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Sanz-García E, Sen S, Slowley RA, Wainwright ME, Deshpande MS, Iudin A, Sahni G, Salavert Torres J, Hirshberg M, Mak L, Nadzirin N, Armstrong DR, Clark AR, Smart OS, Korir PK, Kleywegt GJ.

Nucleic Acids Res, 2016

doi:10.1093/nar/gkv1047.

PDBe: searching the Protein Data Bank

Sen S, Mukhopadhyay A.

2015

doi:10.6019/tol.pdbe-sea-t.2015.00001.1.

PDBe: Searching for biological macromolecular structures

Armstrong DR.

2015

doi:10.6019/tol.pdbe-intr-w.2015.00001.1.

Biomacromolecular structures

Argasinska J, Symmons MF, Gutmanas A, Kleywegt GJ, .

2011

doi:10.6019/tol.bms.2011.00001.1.