PDBe: improved findability of macromolecular structure data in
the PDB

J 2020

PDBe: improved findability of macromolecular structure data in the PDB

ARMSTRONG, David R.; John M. BERRISFORD; Matthew J. CONROY; Aleksandras GUTMANAS; Stephen ANYANGO et al.

Základní údaje

Originální název

PDBe: improved findability of macromolecular structure data in the PDB

Autoři

Vydání

Nucleic acids research, Oxford, Oxford University Press, 2020, 0305-1048

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 16.971

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/20:00117897

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

PDBe; Structural Biology; Molecular Graphics; Data Curation

Štítky

143160, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 6. 3. 2021 12:13, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition, curation, validation, archiving and dissemination of macromolecular structure data. PDBe supports diverse research communities in their use of macromolecular structures by enriching the PDB data and by providing advanced tools and services for effective data access, visualization and analysis. This paper details the enrichment of data at PDBe, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors. PDBe has developed an advanced search facility with similar to 100 data categories and sequence searches. New features have been included in the LiteMol viewer at PDBe, with updated visualization of carbohydrates and nucleic acids. Small molecules are now mapped more extensively to external databases and their visual representation has been enhanced. These advances help users to more easily find and interpret macromolecular structure data in order to solve scientific problems.

Návaznosti

EF16_013/0001777, projekt VaV

Název: ELIXIR-CZ: Budování kapacit

Citovat

ARMSTRONG, David R.; John M. BERRISFORD; Matthew J. CONROY; Aleksandras GUTMANAS; Stephen ANYANGO; Preeti CHOUDHARY; Alice R. CLARK; Jose M. DANA; Mandar DESHPANDE; Roisin DUNLOP; Paul GANE; Romana GÁBOROVÁ; Deepti GUPTA; Pauline HASLAM; Jaroslav KOČA; Lora MAK; Saqib MIR; Abhik MUKHOPADHYAY; Nurul NADZIRIN; Sreenath NAIR; Typhaine PAYSAN-LAFOSSE; Lukas PRAVDA; David SEHNAL; Osman SALIH; Oliver SMART; James TOLCHARD; Mihaly VARADI; Radka SVOBODOVÁ; Hossam ZAKI; Gerard J. KLEYWEGT a Sameer VELANKAR. PDBe: improved findability of macromolecular structure data in the PDB. Nucleic acids research. Oxford: Oxford University Press, 2020, roč. 48, D1, s. "D335"-"D343", 9 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkz990.

@article{1730685,
   author = {Armstrong, David R. and Berrisford, John M. and Conroy, Matthew J. and Gutmanas, Aleksandras and Anyango, Stephen and Choudhary, Preeti and Clark, Alice R. and Dana, Jose M. and Deshpande, Mandar and Dunlop, Roisin and Gane, Paul and Gáborová, Romana and Gupta, Deepti and Haslam, Pauline and Koča, Jaroslav and Mak, Lora and Mir, Saqib and Mukhopadhyay, Abhik and Nadzirin, Nurul and Nair, Sreenath and PaysanandLafosse, Typhaine and Pravda, Lukas and Sehnal, David and Salih, Osman and Smart, Oliver and Tolchard, James and Varadi, Mihaly and Svobodová, Radka and Zaki, Hossam and Kleywegt, Gerard J. and Velankar, Sameer},
   article_location = {Oxford},
   article_number = {D1},
   doi = {https://doi.org/10.1093/nar/gkz990},
   keywords = {PDBe; Structural Biology; Molecular Graphics; Data Curation},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic acids research},
   title = {PDBe: improved findability of macromolecular structure data in the PDB},
   url = {https://doi.org/10.1093/nar/gkz990},
   volume = {48},
   year = {2020}
}

TY  - JOUR
ID  - 1730685
AU  - 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 - Gáborová, Romana - Gupta, Deepti - Haslam, Pauline - Koča, 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 - Svobodová, Radka - Zaki, Hossam - Kleywegt, Gerard J. - Velankar, Sameer
PY  - 2020
TI  - PDBe: improved findability of macromolecular structure data in the PDB
JF  - Nucleic acids research
VL  - 48
IS  - D1
SP  - "D335"-"D343"
EP  - "D335"-"D343"
PB  - Oxford University Press
SN  - 03051048
KW  - PDBe
KW  - Structural Biology
KW  - Molecular Graphics
KW  - Data Curation
UR  - https://doi.org/10.1093/nar/gkz990
L2  - https://doi.org/10.1093/nar/gkz990
N2  - The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition, curation, validation, archiving and dissemination of macromolecular structure data. PDBe supports diverse research communities in their use of macromolecular structures by enriching the PDB data and by providing advanced tools and services for effective data access, visualization and analysis. This paper details the enrichment of data at PDBe, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors. PDBe has developed an advanced search facility with similar to 100 data categories and sequence searches. New features have been included in the LiteMol viewer at PDBe, with updated visualization of carbohydrates and nucleic acids. Small molecules are now mapped more extensively to external databases and their visual representation has been enhanced. These advances help users to more easily find and interpret macromolecular structure data in order to solve scientific problems.
ER  -

ARMSTRONG, David R.; John M. BERRISFORD; Matthew J. CONROY; Aleksandras GUTMANAS; Stephen ANYANGO; Preeti CHOUDHARY; Alice R. CLARK; Jose M. DANA; Mandar DESHPANDE; Roisin DUNLOP; Paul GANE; Romana GÁBOROVÁ; Deepti GUPTA; Pauline HASLAM; Jaroslav KOČA; Lora MAK; Saqib MIR; Abhik MUKHOPADHYAY; Nurul NADZIRIN; Sreenath NAIR; Typhaine PAYSAN-LAFOSSE; Lukas PRAVDA; David SEHNAL; Osman SALIH; Oliver SMART; James TOLCHARD; Mihaly VARADI; Radka SVOBODOVÁ; Hossam ZAKI; Gerard J. KLEYWEGT a Sameer VELANKAR. PDBe: improved findability of macromolecular structure data in the PDB. \textit{Nucleic acids research}. Oxford: Oxford University Press, 2020, roč.~48, D1, s.~''D335''-''D343'', 9 s. ISSN~0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkz990.

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