RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

被引：446

作者：

Burley, Stephen K. ^{[1
,2
,3
,4
,5
]}

Bhikadiya, Charmi ^{[5
]}

Bi, Chunxiao ^{[5
]}

Bittrich, Sebastian ^{[5
]}

Chao, Henry ^{[1
,2
]}

Chen, Li ^{[1
,2
]}

Craig, Paul A. ^{[6
]}

Crichlow, Gregg, V ^{[1
,2
]}

Dalenberg, Kenneth ^{[1
,2
]}

Duarte, Jose M. ^{[5
]}

Dutta, Shuchismita ^{[1
,2
,3
]}

Fayazi, Maryam ^{[1
,2
]}

Feng, Zukang ^{[1
,2
]}

Flatt, Justin W. ^{[1
,2
]}

Ganesan, Sai ^{[7
]}

Ghosh, Sutapa ^{[1
,2
]}

Goodsell, David S. ^{[1
,2
,3
,8
]}

Green, Rachel Kramer ^{[1
,2
]}

Guranovic, Vladimir ^{[1
,2
]}

Henry, Jeremy ^{[5
]}

Hudson, Brian P. ^{[1
,2
]}

Khokhriakov, Igor ^{[5
]}

Lawson, Catherine L. ^{[1
,2
]}

Liang, Yuhe ^{[1
,2
]}

Lowe, Robert ^{[1
,2
]}

Peisach, Ezra ^{[1
,2
]}

Persikova, Irina ^{[1
,2
]}

Piehl, Dennis W. ^{[1
,2
]}

Rose, Yana ^{[5
]}

Sali, Andrej

Segura, Joan ^{[5
]}

Sekharan, Monica ^{[1
,2
]}

Shao, Chenghua ^{[1
,2
]}

Vallat, Brinda ^{[1
,2
]}

Voigt, Maria ^{[1
,2
]}

Webb, Ben

Westbrook, John D. ^{[1
,2
,3
]}

Whetstone, Shamara ^{[1
,2
]}

Young, Jasmine Y. ^{[1
,2
]}

Zalevsky, Arthur

Zardecki, Christine ^{[1
,2
]}

机构：

[1] Rutgers State Univ, Res Collaboratory Struct Bioinformat Prot Data Ban, Piscataway, NJ 08854 USA

[2] Rutgers State Univ, Inst Quantitat Biomed, Piscataway, NJ 08854 USA

[3] Rutgers Canc Inst New Jersey, New Brunswick, NJ 08901 USA

[4] Rutgers State Univ, Dept Chem & Chem Biol, Piscataway, NJ 08854 USA

[5] Univ Calif San Diego, San Diego Supercomp Ctr, Res Collaboratory Struct Bioinformat Prot Data Ban, La Jolla, CA 92093 USA

[6] Rochester Inst Technol, Sch Chem & Mat Sci, Rochester, NY 14623 USA

[7] Univ Calif San Francisco, Quantitat Biosci Inst, Dept Bioengn & Therapeut Sci, Dept Pharmaceut Chem,Res Collaboratory Struct Bioi, San Francisco, CA 94158 USA

[8] Scripps Res Inst, Dept Integrat Struct & Computat Biol, La Jolla, CA 92037 USA

来源：

NUCLEIC ACIDS RESEARCH | 2023年 / 51卷 / D1期

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

STRUCTURE PREDICTION; BIOLOGICAL MACROMOLECULES; RESOURCE; INFORMATION; VALIDATION; BIOTECHNOLOGY; VISUALIZATION; ANNOTATION; DEPOSITION; FAMILIES;

D O I：

10.1093/nar/gkac1077

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to similar to 200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a 'living data resource.' Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

引用

页码：D488 / D508

页数：21

共 128 条

[1] The GTEx Consortium atlas of genetic regulatory effects across human tissues [J].

Aguet, Francois ;

Barbeira, Alvaro N. ;

Bonazzola, Rodrigo ;

Brown, Andrew ;

Castel, Stephane E. ;

Jo, Brian ;

Kasela, Silva ;

Kim-Hellmuth, Sarah ;

Liang, Yanyu ;

Parsana, Princy ;

Flynn, Elise ;

Fresard, Laure ;

Gamazon, Eric R. ;

Hamel, Andrew R. ;

He, Yuan ;

Hormozdiari, Farhad ;

Mohammadi, Pejman ;

Munoz-Aguirre, Manuel ;

Ardlie, Kristin G. ;

Battle, Alexis ;

Bonazzola, Rodrigo ;

Brown, Christopher D. ;

Cox, Nancy ;

Dermitzakis, Emmanouil T. ;

Engelhardt, Barbara E. ;

Garrido-Martin, Diego ;

Gay, Nicole R. ;

Getz, Gad ;

Guigo, Roderic ;

Hamel, Andrew R. ;

Handsaker, Robert E. ;

He, Yuan ;

Hoffman, Paul J. ;

Hormozdiari, Farhad ;

Im, Hae Kyung ;

Jo, Brian ;

Kasela, Silva ;

Kashin, Seva ;

Kim-Hellmuth, Sarah ;

Kwong, Alan ;

Lappalainen, Tuuli ;

Li, Xiao ;

Liang, Yanyu ;

MacArthur, Daniel G. ;

Mohammadi, Pejman ;

Montgomery, Stephen B. ;

Munoz-Aguirre, Manuel ;

Rouhana, John M. ;

Hormozdiari, Farhad ;

Im, Hae Kyung .

SCIENCE, 2020, 369 (6509) :1318-1330

[2] Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures [J].

Ahmed, Aqeel ;

Smith, Richard D. ;

Clark, Jordan J. ;

Dunbar, James B., Jr. ;

Carlson, Heather A. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D465-D469

[3] Target highlights in CASP14: Analysis of models by structure providers [J].

Alexander, Leila T. ;

Lepore, Rosalba ;

Kryshtafovych, Andriy ;

Adamopoulos, Athanassios ;

Alahuhta, Markus ;

Arvin, Ann M. ;

Bomble, Yannick J. ;

Bottcher, Bettina ;

Breyton, Cecile ;

Chiarini, Valerio ;

Chinnam, Naga Babu ;

Chiu, Wah ;

Fidelis, Krzysztof ;

Grinter, Rhys ;

Gupta, Gagan D. ;

Hartmann, Marcus D. ;

Hayes, Christopher S. ;

Heidebrecht, Tatjana ;

Ilari, Andrea ;

Joachimiak, Andrzej ;

Kim, Youngchang ;

Linares, Romain ;

Lovering, Andrew L. ;

Lunin, Vladimir V. ;

Lupas, Andrei N. ;

Makbul, Cihan ;

Michalska, Karolina ;

Moult, John ;

Mukherjee, Prasun K. ;

Nutt, William Sam ;

Oliver, Stefan L. ;

Perrakis, Anastassis ;

Stols, Lucy ;

Tainer, John A. ;

Topf, Maya ;

Tsutakawa, Susan E. ;

Valdivia-Delgado, Mauricio ;

Schwede, Torsten .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2021, 89 (12) :1647-1672

[4]

Anderson W., 2017, BIORXIV, DOI [10.1101/110825v3, DOI 10.1101/110825V3]

[5] A global coalition to sustain core data [J].

Anderson, Warwick P. .

NATURE, 2017, 543 (7644) :179-179

[6] The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures [J].

Andreeva, Antonina ;

Kulesha, Eugene ;

Gough, Julian ;

Murzin, Alexey G. .

NUCLEIC ACIDS RESEARCH, 2020, 48 (D1) :D376-D382

[7] SCOP2 prototype: a new approach to protein structure mining [J].

Andreeva, Antonina ;

Howorth, Dave ;

Chothia, Cyrus ;

Kulesha, Eugene ;

Murzin, Alexey G. .

NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D310-D314

[8] PRINCIPLES THAT GOVERN FOLDING OF PROTEIN CHAINS [J].

ANFINSEN, CB .

SCIENCE, 1973, 181 (4096) :223-230

[9]

Apweiler R, 2004, NUCLEIC ACIDS RES, V32, pD115, DOI [10.1093/nar/gkw1099, 10.1093/nar/gkh131]

[10] PDBe: improved findability of macromolecular structure data in the PDB [J].

Armstrong, David R. ;

Berrisford, John M. ;

Conroy, Matthew J. ;

Gutmanas, Aleksandras ;

Anyango, Stephen ;

Choudhary, Preeti ;

Clark, Alice R. ;

Dana, Jose M. ;

Deshpande, Mandar ;

Dunlop, Roisin ;

Gane, Paul ;

Gaborova, Romana ;

Gupta, Deepti ;

Haslam, Pauline ;

Koca, Jaroslav ;

Mak, Lora ;

Mir, Saqib ;

Mukhopadhyay, Abhik ;

Nadzirin, Nurul ;

Nair, Sreenath ;

Paysan-Lafosse, Typhaine ;

Pravda, Lukas ;

Sehnal, David ;

Salih, Osman ;

Smart, Oliver ;

Tolchard, James ;

Varadi, Mihaly ;

Svobodova-Varekova, Radka ;

Zaki, Hossam ;

Kleywegt, Gerard J. ;

Velankar, Sameer .

NUCLEIC ACIDS RESEARCH, 2020, 48 (D1) :D335-D343

← 1 2 3 4 5 6 7 8 9 10 →