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

S.k Burley ,Miron Livny,Typhaine Paysan-Lafosse,Dmytro Guzenko,Lora Mak,Sameer Velankar,Jaroslav Koča,Osman Salih,Abhik Mukhopadhyay,Takeshi Iwata,Kumaran Baskaran,Vladimir Guranovic,Deepti Gupta,Yumiko Kengaku,Hirofumi Suzuki,Irina Periskova,David Sehnal,Maria Voigt,Ezra Peisach,Yasuyo Ikegawa,Junko Sato,Stephen Anyango,Monica Sekharan,Atsushi Nakagawa,Sutapa Ghosh,Dimitri Maziuk,Reiko Yamashita,Chunxiao Bi,Li Chen,Sreenath Nair,Christine Zardecki,Shuchismita Dutta,Ju Yaen Kim,Takahiro Kudou,Chenghua Shao,Hasumi Cho,Masashi Yokochi,Chris Randle,Rachel Kramer Green,Toshimichi Fujiwara,Yana Valasatava,Romana Gáborová,Robert Lowe,Naohiro Kobayashi,Mandar Deshpande,Yi-Ping Tao,Nurul Nadzirin,Haruki Nakamura,Jasmine Young,Alexander Rose,Ardan Patwardhan,Charmi Bhikadiya,Saqib Mir,Genji Kurisu,Hongyang Yao,Aleksandras Gutmanas,José M Duarte ,Yu-He Liang ,Jeffrey C Hoch ,David Armstrong ,Jonathan R Wedell ,John M Berrisford ,Eldon L Ulrich ,Pedro Romero ,Mihály Váradi ,Marina A Zhuravleva ,L Di Costanzo ,John L Markley ,Lukáš Pravda ,Zhang Feng ,Gert‐Jan Bekker ,Jose M Dana ,Helen M Berman ,David S Goodsell ,Radka Svobodová Vařeková ,Paul J Gane ,Cole H Christie ,Matthew J Conroy ,John D Westbrook ,Gerard J Kleywegt ,Brian P Hudson ,Yannis Ioannidis

doi:10.1093/nar/gky949

Abstract

The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.

Highlights

The Protein Data Bank (PDB, pdb.org) was established in 1971 as the first open-access, molecular data resource in biology [1]
The PDB is universally regarded as a core data resource essential for understanding the functional roles that macromolecules play in biology and medicine
D522 Nucleic Acids Research, 2019, Vol 47, Database issue tem and various methods-specific Worldwide Protein Data Bank (wwPDB) Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive, together with current challenges and future plans

Summary

Introduction

The Protein Data Bank (PDB, pdb.org) was established in 1971 as the first open-access, molecular data resource in biology [1]. D522 Nucleic Acids Research, 2019, Vol 47, Database issue tem and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive, together with current challenges and future plans.

Results

Conclusion