Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

(2020) Alexandra C. Walls et al.   CELL

High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM

(2019) Mark A. Herzik et al.   Nature Communications

Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution

(2019) Xiao Fan et al.   Nature Communications

The subatomic resolution study of laccase inhibition by chloride and fluoride anions using single-crystal serial crystallography: insights into the enzymatic reaction mechanism

(2019) Konstantin M. Polyakov et al.   Acta Crystallographica Section D-Structural Biology

The N-Glycosylation Processing Potential of the Mammalian Golgi Apparatus

(2019) Peter Fisher et al.   Frontiers in Cell and Developmental Biology

Structural glycobiology in the age of electron cryo-microscopy

(2019) Mihaela Atanasova et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure and Immune Recognition of the HIV Glycan Shield

(2018) Max Crispin et al.   Annual Review of Biophysics

Structure of the Lassa virus glycan shield provides a model for immunological resistance

(2018) Yasunori Watanabe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

(2018) Tristan Ian Croll   Acta Crystallographica Section D-Structural Biology

CCP4i2: the new graphical user interface to the CCP4 program suite

(2018) Liz Potterton et al.   Acta Crystallographica Section D-Structural Biology

Structural analysis of glycoproteins: building N-linked glycans with Coot

(2018) Paul Emsley et al.   Acta Crystallographica Section D-Structural Biology

African trypanosomes evade immune clearance by O-glycosylation of the VSG surface coat

(2018) Jason Pinger et al.   Nature Microbiology

Making glycoproteins a little bit sweeter with PDB-REDO

(2018) Bart van Beusekom et al.   Acta Crystallographica Section F-Structural Biology Communications

GlycanFormatConverter: a conversion tool for translating the complexities of glycans

(2018) Shinichiro Tsuchiya et al.   BIOINFORMATICS

GlyConnect: Glycoproteomics Goes Visual, Interactive, and Analytical

(2018) Davide Alocci et al.   JOURNAL OF PROTEOME RESEARCH

Automatically Fixing Errors in Glycoprotein Structures with Rosetta

(2018) Brandon Frenz et al.   STRUCTURE

GlyTouCan: an accessible glycan structure repository

(2017) Michael Tiemeyer et al.   GLYCOBIOLOGY

WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures

(2017) Masaaki Matsubara et al.   Journal of Chemical Information and Modeling

Strategies for carbohydrate model building, refinement and validation

(2017) Jon Agirre   Acta Crystallographica Section D-Structural Biology

X-ray and EM structures of a natively glycosylated HIV-1 envelope trimer

(2017) Harry B. Gristick et al.   Acta Crystallographica Section D-Structural Biology

How cryo-electron microscopy and X-ray crystallography complement each other

(2016) Hong-Wei Wang et al.   PROTEIN SCIENCE

A Primer to Single-Particle Cryo-Electron Microscopy

(2015) Yifan Cheng et al.   CELL

Molecular dynamics simulations of large macromolecular complexes

(2015) Juan R Perilla et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Carbohydrate anomalies in the PDB

(2015) Jon Agirre et al.   Nature Chemical Biology

Privateer: software for the conformational validation of carbohydrate structures

(2015) Jon Agirre et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GlyTouCan 1.0 – The international glycan structure repository

(2015) Kiyoko Aoki-Kinoshita et al.   NUCLEIC ACIDS RESEARCH

Privateer: software for the conformational validation of carbohydrate structures

(2015) Jon Agirre et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Glycans Instructing Immunity: The Emerging Role of Altered Glycosylation in Clinical Immunology

(2015) Jonathan J. Lyons et al.   Frontiers in Pediatrics

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank

(2014) John D. Westbrook et al.   BIOINFORMATICS

The Chaperone Activity of Clusterin is Dependent on Glycosylation and Redox Environment

(2014) Philipp Rohne et al.   CELLULAR PHYSIOLOGY AND BIOCHEMISTRY

WURCS: The Web3 Unique Representation of Carbohydrate Structures

(2014) Kenichi Tanaka et al.   Journal of Chemical Information and Modeling

Receptor mimicry by antibody F045–092 facilitates universal binding to the H3 subtype of influenza virus

(2014) Peter S. Lee et al.   Nature Communications

UniCarbKB: building a knowledge platform for glycoproteomics

(2013) Matthew P. Campbell et al.   NUCLEIC ACIDS RESEARCH

The Influence of N-Linked Glycans on the Molecular Dynamics of the HIV-1 gp120 V3 Loop

(2013) Natasha T. Wood et al.   PLoS One

Effective Use of Mass Spectrometry for Glycan and Glycopeptide Structural Analysis

(2012) Nancy Leymarie et al.   ANALYTICAL CHEMISTRY

Potential roles of N-glycosylation in cell adhesion

(2012) Jianguo Gu et al.   GLYCOCONJUGATE JOURNAL

UniCarb-DB: a database resource for glycomic discovery

(2011) Catherine A. Hayes et al.   BIOINFORMATICS

Glycosylation, galectins and cellular signaling

(2011) Cecile Boscher et al.   CURRENT OPINION IN CELL BIOLOGY

EUROCarbDB: An open-access platform for glycoinformatics

(2010) C.-W. von der Lieth et al.   GLYCOBIOLOGY

GlycomeDB – integration of open-access carbohydrate structure databases

(2008) René Ranzinger et al.   BMC BIOINFORMATICS

GlycoCT—a unifying sequence format for carbohydrates

(2008) S. Herget et al.   CARBOHYDRATE RESEARCH

GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans†

(2008) Alessio Ceroni et al.   JOURNAL OF PROTEOME RESEARCH

Structure of influenza hemagglutinin in complex with an inhibitor of membrane fusion

(2008) R. J. Russell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA