PMID- 26581513
OWN - NLM
STAT- In-Data-Review
DA  - 20151120
IS  - 1545-9985 (Electronic)
IS  - 1545-9985 (Linking)
VI  - 22
IP  - 11
DP  - 2015 Nov 4
TI  - Privateer: software for the conformational validation of carbohydrate structures.
PG  - 833-4
LID - 10.1038/nsmb.3115 [doi]
FAU - Agirre, Jon
AU  - Agirre J
AUID- ORCID: http://orcid.org/0000-0002-1086-0253
AD  - Department of Chemistry, University of York, York, UK.
FAU - Iglesias-Fernandez, Javier
AU  - Iglesias-Fernandez J
AD  - Departament de Quimica Organica and Institut de Quimica Teorica i Computacional
      (IQTCUB), Universitat de Barcelona, Barcelona, Spain.
FAU - Rovira, Carme
AU  - Rovira C
AD  - Departament de Quimica Organica and Institut de Quimica Teorica i Computacional
      (IQTCUB), Universitat de Barcelona, Barcelona, Spain.
AD  - Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Spain.
FAU - Davies, Gideon J
AU  - Davies GJ
AUID- ORCID: http://orcid.org/0000-0002-7343-776X
AD  - Department of Chemistry, University of York, York, UK.
FAU - Wilson, Keith S
AU  - Wilson KS
AD  - Department of Chemistry, University of York, York, UK.
FAU - Cowtan, Kevin D
AU  - Cowtan KD
AUID- ORCID: http://orcid.org/0000-0002-0189-1437
AD  - Department of Chemistry, University of York, York, UK.
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Nat Struct Mol Biol
JT  - Nature structural & molecular biology
JID - 101186374
SB  - IM
EDAT- 2015/11/20 06:00
MHDA- 2015/11/20 06:00
CRDT- 2015/11/20 06:00
AID - nsmb.3115 [pii]
AID - 10.1038/nsmb.3115 [doi]
PST - ppublish
SO  - Nat Struct Mol Biol. 2015 Nov 4;22(11):833-4. doi: 10.1038/nsmb.3115.



PMID- 25885951
OWN - NLM
STAT- MEDLINE
DA  - 20150418
DCOM- 20150626
LR  - 20150820
IS  - 1552-4469 (Electronic)
IS  - 1552-4450 (Linking)
VI  - 11
IP  - 5
DP  - 2015 May
TI  - Carbohydrate anomalies in the PDB.
PG  - 303
LID - 10.1038/nchembio.1798 [doi]
FAU - Agirre, Jon
AU  - Agirre J
AUID- ORCID: 0000000210860253
AD  - York Structural Biology Laboratory, Department of Chemistry, The University of
      York, UK.
FAU - Davies, Gideon
AU  - Davies G
AUID- ORCID: 000000027343776X
AD  - York Structural Biology Laboratory, Department of Chemistry, The University of
      York, UK.
FAU - Wilson, Keith
AU  - Wilson K
AD  - York Structural Biology Laboratory, Department of Chemistry, The University of
      York, UK.
FAU - Cowtan, Kevin
AU  - Cowtan K
AD  - York Structural Biology Laboratory, Department of Chemistry, The University of
      York, UK.
LA  - eng
GR  - BB/K008153/1/Biotechnology and Biological Sciences Research Council/United
      Kingdom
PT  - Letter
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Nat Chem Biol
JT  - Nature chemical biology
JID - 101231976
RN  - 0 (Carbohydrates)
SB  - IM
EIN - Nat Chem Biol. 2015 Jul;11(7):532. PMID: 26083072
MH  - Carbohydrates/*chemistry
MH  - *Databases, Protein
MH  - Software
EDAT- 2015/04/18 06:00
MHDA- 2015/06/27 06:00
CRDT- 2015/04/18 06:00
AID - nchembio.1798 [pii]
AID - 10.1038/nchembio.1798 [doi]
PST - ppublish
SO  - Nat Chem Biol. 2015 May;11(5):303. doi: 10.1038/nchembio.1798.



PMID- 33093930
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20210203
IS  - 1860-5397 (Print)
IS  - 1860-5397 (Electronic)
IS  - 1860-5397 (Linking)
VI  - 16
DP  - 2020
TI  - Leveraging glycomics data in glycoprotein 3D structure validation with Privateer.
PG  - 2523-2533
LID - 10.3762/bjoc.16.204 [doi]
AB  - The heterogeneity, mobility and complexity of glycans in glycoproteins have been, 
      and currently remain, significant challenges in structural biology. These aspects 
      present unique problems to the two most prolific techniques: X-ray crystallography 
      and cryo-electron microscopy. At the same time, advances in mass spectrometry have 
      made it possible to get deeper insights on precisely the information that is most 
      difficult to recover by structure solution methods: the full-length glycan 
      composition, including linkage details for the glycosidic bonds. The developments 
      have given rise to glycomics. Thankfully, several large scale glycomics initiatives 
      have stored results in publicly available databases, some of which can be accessed 
      through API interfaces. In the present work, we will describe how the Privateer 
      carbohydrate structure validation software has been extended to harness results from 
      glycomics projects, and its use to greatly improve the validation of 3D glycoprotein 
      structures.
CI  - Copyright © 2020, Bagdonas et al.; licensee Beilstein-Institut.
FAU - Bagdonas, Haroldas
AU  - Bagdonas H
AUID- ORCID: 0000-0001-5028-4847
AD  - York Structural Biology Laboratory, Department of Chemistry, University of York, 
      Wentworth Way, York, YO10 5DD, UK.
FAU - Ungar, Daniel
AU  - Ungar D
AUID- ORCID: 0000-0002-9852-6160
AD  - Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
FAU - Agirre, Jon
AU  - Agirre J
AUID- ORCID: 0000-0002-1086-0253
AD  - York Structural Biology Laboratory, Department of Chemistry, University of York, 
      Wentworth Way, York, YO10 5DD, UK.
LA  - eng
PT  - Journal Article
DEP - 20201009
TA  - Beilstein J Org Chem
JT  - Beilstein journal of organic chemistry
JID - 101250746
PMC - PMC7554661
OTO - NOTNLM
OT  - Privateer
OT  - X-ray crystallography
OT  - electron cryomicroscopy
OT  - glycoinformatics
OT  - glycomics
EDAT- 2020/10/24 06:00
MHDA- 2020/10/24 06:01
CRDT- 2020/10/23 05:57
PHST- 2020/07/18 00:00 [received]
PHST- 2020/10/06 00:00 [accepted]
PHST- 2020/10/23 05:57 [entrez]
PHST- 2020/10/24 06:00 [pubmed]
PHST- 2020/10/24 06:01 [medline]
AID - 10.3762/bjoc.16.204 [doi]
PST - epublish
SO  - Beilstein J Org Chem. 2020 Oct 9;16:2523-2533. doi: 10.3762/bjoc.16.204. eCollection 
      2020.