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

J 2018

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

MIR, S.; Y. ALHROUB; S. ANYANGO; D.R. ARMSTRONG; J.M. BERRISFORD et al.

Základní údaje

Originální název

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

Autoři

Vydání

Nucleic Acids Research, Oxford, Oxford University Press, 2018, 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

Impakt faktor

Impact factor: 11.147

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/18:00106678

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

MACROMOLECULAR STRUCTURES; VISUALIZATION; SEQUENCES; ARCHIVE; ANNOTATIONS; DEPOSITION; FRAMEWORK; RESOURCE; TAXONOMY; SYSTEM

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 21. 3. 2019 08:22, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.

Citovat

MIR, S.; Y. ALHROUB; S. ANYANGO; D.R. ARMSTRONG; J.M. BERRISFORD; A.R. CLARK; M.J. CONROY; J.M. DANA; M. DESHPANDE; D. GUPTA; A. GUTMANAS; P. HASLAM; L. MAK; A. MUKHOPADHYAY; N. NADZIRIN; T. PAYSAN-LAFOSSE; David SEHNAL; S. SEN; O.S. SMART; M. VARADI; G.J. KLEYWEGT a S. VELANKAR. PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. Nucleic Acids Research. Oxford: Oxford University Press, 2018, roč. 46, D1, s. "D486"-"D492", 7 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkx1070.

@article{1508617,
   author = {Mir, S. and Alhroub, Y. and Anyango, S. and Armstrong, D.R. and Berrisford, J.M. and Clark, A.R. and Conroy, M.J. and Dana, J.M. and Deshpande, M. and Gupta, D. and Gutmanas, A. and Haslam, P. and Mak, L. and Mukhopadhyay, A. and Nadzirin, N. and PaysanandLafosse, T. and Sehnal, David and Sen, S. and Smart, O.S. and Varadi, M. and Kleywegt, G.J. and Velankar, S.},
   article_location = {Oxford},
   article_number = {D1},
   doi = {https://doi.org/10.1093/nar/gkx1070},
   keywords = {MACROMOLECULAR STRUCTURES; VISUALIZATION; SEQUENCES; ARCHIVE; ANNOTATIONS; DEPOSITION; FRAMEWORK; RESOURCE; TAXONOMY; SYSTEM},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {PDBe: towards reusable data delivery infrastructure at protein data bank in Europe},
   volume = {46},
   year = {2018}
}

TY  - JOUR
ID  - 1508617
AU  - Mir, S. - Alhroub, Y. - Anyango, S. - Armstrong, D.R. - Berrisford, J.M. - Clark, A.R. - Conroy, M.J. - Dana, J.M. - Deshpande, M. - Gupta, D. - Gutmanas, A. - Haslam, P. - Mak, L. - Mukhopadhyay, A. - Nadzirin, N. - Paysan-Lafosse, T. - Sehnal, David - Sen, S. - Smart, O.S. - Varadi, M. - Kleywegt, G.J. - Velankar, S.
PY  - 2018
TI  - PDBe: towards reusable data delivery infrastructure at protein data bank in Europe
JF  - Nucleic Acids Research
VL  - 46
IS  - D1
SP  - "D486"-"D492"
EP  - "D486"-"D492"
PB  - Oxford University Press
SN  - 03051048
KW  - MACROMOLECULAR STRUCTURES
KW  - VISUALIZATION
KW  - SEQUENCES
KW  - ARCHIVE
KW  - ANNOTATIONS
KW  - DEPOSITION
KW  - FRAMEWORK
KW  - RESOURCE
KW  - TAXONOMY
KW  - SYSTEM
N2  - The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.
ER  -

MIR, S.; Y. ALHROUB; S. ANYANGO; D.R. ARMSTRONG; J.M. BERRISFORD; A.R. CLARK; M.J. CONROY; J.M. DANA; M. DESHPANDE; D. GUPTA; A. GUTMANAS; P. HASLAM; L. MAK; A. MUKHOPADHYAY; N. NADZIRIN; T. PAYSAN-LAFOSSE; David SEHNAL; S. SEN; O.S. SMART; M. VARADI; G.J. KLEYWEGT a S. VELANKAR. PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2018, roč.~46, D1, s.~''D486''-''D492'', 7 s. ISSN~0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkx1070.

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