The case for post-predictional modifications in the AlphaFold Protein Structure Database

被引:59
作者
Bagdonas, Haroldas [1 ]
Fogarty, Carl A. [2 ,3 ]
Fadda, Elisa [2 ,3 ]
Agirre, Jon [1 ]
机构
[1] Univ York, Dept Chem, York Struct Biol Lab, York, N Yorkshire, England
[2] Maynooth Univ, Dept Chem, Maynooth, Kildare, Ireland
[3] Maynooth Univ, Hamilton Inst, Maynooth, Kildare, Ireland
关键词
VALIDATION;
D O I
10.1038/s41594-021-00680-9
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
引用
收藏
页码:869 / 870
页数:2
相关论文
共 13 条
[1]   Privateer: software for the conformational validation of carbohydrate structures [J].
Agirre, Jon ;
Iglesias-Fernandez, Javier ;
Rovira, Carme ;
Davies, Gideon J. ;
Wilson, Keith S. ;
Cowtan, Kevin D. .
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2015, 22 (11) :833-834
[2]   Determination of glycosylation sites and site-specific heterogeneity in glycoproteins [J].
An, Hyun Joo ;
Froehlich, John W. ;
Lebrilla, Carlito B. .
CURRENT OPINION IN CHEMICAL BIOLOGY, 2009, 13 (04) :421-426
[3]   Structural glycobiology in the age of electron cryo-microscopy [J].
Atanasova, Mihaela ;
Bagdonas, Haroldas ;
Agirre, Jon .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2020, 62 :70-78
[4]   Leveraging glycomics data in glycoprotein 3D structure validation with Privateer [J].
Bagdonas, Haroldas ;
Ungar, Daniel ;
Agirre, Jon .
BEILSTEIN JOURNAL OF ORGANIC CHEMISTRY, 2020, 16 :2523-2533
[5]   Announcing the worldwide Protein Data Bank [J].
Berman, H ;
Henrick, K ;
Nakamura, H .
NATURE STRUCTURAL BIOLOGY, 2003, 10 (12) :980-980
[6]   Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein [J].
Casalino, Lorenzo ;
Gaieb, Zied ;
Goldsmith, Jory A. ;
Hjorth, Christy K. ;
Dommer, Abigail C. ;
Harbison, Aoife M. ;
Fogarty, Carl A. ;
Barros, Emilia P. ;
Taylor, Bryn C. ;
McLellan, Jason S. ;
Fadda, Elisa ;
Amaro, Rommie E. .
ACS CENTRAL SCIENCE, 2020, 6 (10) :1722-1734
[7]   Oligomannose N-Glycans 3D Architecture and Its Response to the FcγRIIIa Structural Landscape [J].
Fogarty, Carl A. ;
Fadda, Elisa .
JOURNAL OF PHYSICAL CHEMISTRY B, 2021, 125 (10) :2607-2616
[8]   Carbohydrate-Aromatic Interactions in Proteins [J].
Hudson, Kieran L. ;
Bartlett, Gail J. ;
Diehl, Roger C. ;
Agirre, Jon ;
Gallagher, Timothy ;
Kiessling, Laura L. ;
Woolfson, Derek N. .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2015, 137 (48) :15152-15160
[9]   Highly accurate protein structure prediction with AlphaFold [J].
Jumper, John ;
Evans, Richard ;
Pritzel, Alexander ;
Green, Tim ;
Figurnov, Michael ;
Ronneberger, Olaf ;
Tunyasuvunakool, Kathryn ;
Bates, Russ ;
Zidek, Augustin ;
Potapenko, Anna ;
Bridgland, Alex ;
Meyer, Clemens ;
Kohl, Simon A. A. ;
Ballard, Andrew J. ;
Cowie, Andrew ;
Romera-Paredes, Bernardino ;
Nikolov, Stanislav ;
Jain, Rishub ;
Adler, Jonas ;
Back, Trevor ;
Petersen, Stig ;
Reiman, David ;
Clancy, Ellen ;
Zielinski, Michal ;
Steinegger, Martin ;
Pacholska, Michalina ;
Berghammer, Tamas ;
Bodenstein, Sebastian ;
Silver, David ;
Vinyals, Oriol ;
Senior, Andrew W. ;
Kavukcuoglu, Koray ;
Kohli, Pushmeet ;
Hassabis, Demis .
NATURE, 2021, 596 (7873) :583-+
[10]   Highly accurate protein structure prediction for the human proteome [J].
Tunyasuvunakool, Kathryn ;
Adler, Jonas ;
Wu, Zachary ;
Green, Tim ;
Zielinski, Michal ;
Zidek, Augustin ;
Bridgland, Alex ;
Cowie, Andrew ;
Meyer, Clemens ;
Laydon, Agata ;
Velankar, Sameer ;
Kleywegt, Gerard J. ;
Bateman, Alex ;
Evans, Richard ;
Pritzel, Alexander ;
Figurnov, Michael ;
Ronneberger, Olaf ;
Bates, Russ ;
Kohl, Simon A. A. ;
Potapenko, Anna ;
Ballard, Andrew J. ;
Romera-Paredes, Bernardino ;
Nikolov, Stanislav ;
Jain, Rishub ;
Clancy, Ellen ;
Reiman, David ;
Petersen, Stig ;
Senior, Andrew W. ;
Kavukcuoglu, Koray ;
Birney, Ewan ;
Kohli, Pushmeet ;
Jumper, John ;
Hassabis, Demis .
NATURE, 2021, 596 (7873) :590-+