A5040965854- Glycosylation and Glycoproteins Research
- Enzyme Structure and Function
- Genomics and Phylogenetic Studies
- Carbohydrate Chemistry and Synthesis
- Protein Structure and Dynamics
- Biochemical and Molecular Research
- Big Data and Business Intelligence
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Biopolymer Synthesis and Applications
- Food Quality and Safety Studies
- Advanced Electron Microscopy Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Galectins and Cancer Biology
University of York
2019-2025
The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with mission to develop, test, distribute and promote software for macromolecular crystallography. CCP suite multiplatform collection of programs brought together by familiar execution routines, set common libraries graphical interfaces. has experienced several considerable changes since its last reference article, involving new infrastructure, original This which intended as general literature citation...
Abstract Tryptophan mannosylation, the covalent addition of an α‐ᴅ‐mannose sugar to a tryptophan side chain, is post‐translational modification (PTM) that can affect protein stability, folding, and interactions. Compared other forms glycosylation, it relatively uncommon but affected by conformational anomalies modeling errors similar those seen in N ‐ O ‐glycans Protein Data Bank (PDB). In this work, we report methods for detecting, building, improving mannose structures linked tryptophans....
Owing to the difficulties associated with working carbohydrates, validating glycan 3D structures prior deposition into Protein Data Bank has become a staple of structure-solution pipeline. The Privateer software provides integrative methods for validation, analysis, refinement and graphical representation atomic glycans, both as ligands protein modifiers. While is free software, it requires users install any structural biology suites that support or build from source code. Here, web app...
The oligosaccharides in N -glycosylation provide key structural and functional contributions to a glycoprotein. These are dependent on the composition overall conformation of glycans. Privateer software allows biologists evaluate improve atomic structures carbohydrates, including -glycans; this has recently been extended check glycan through use glycomics data. Here, broadening scope analyse validate -glycans is presented, focusing newly compiled set glycosidic linkage torsional preferences...
The remediation of the carbohydrate data Protein Data Bank (PDB) has brought numerous enhancements to findability and interpretability deposited glycan structures, yet crucial quality indicators are either missing or hard find on PDB pages. Without a way access wider glycochemical context, problematic structures may be taken as fact by keen but inexperienced scientists. Privateer software is validation analysis tool that provides number metrics links external experimental resources, allowing...
The heterogeneity, mobility and complexity of glycans in glycoproteins have been, currently remain, significant challenges structural biology. These aspects present unique problems to the two most prolific techniques: X-ray crystallography cryo-electron microscopy. At same time, advances mass spectrometry made it possible get deeper insights on precisely information that is difficult recover by structure solution methods: full-length glycan composition, including linkage details for...
The remediation of the carbohydrate data Protein Data Bank (PDB) has brought numerous enhancements to findability and interpretability deposited glycan structures, yet crucial quality indicators are either missing or hard find on PDB pages. Without a way access wider glyco-chemical context, problematic structures may be taken as fact by keen but inexperienced scientists. Privateer software is validation analysis tool that provides number metrics links external experimental resources,...
The methodology underpinning the construction, refinement, validation and analysis of atomic models glycoproteins protein-carbohydrate complexes has received a long-overdue boost in last five years. This is very timely development, as resolution revolution electron cryo-microscopy now routinely delivering structures key glycomedical importance, with three-dimensional precision where X-ray crystallographic methods have traditionally floundered. review will focus on new software developments...
The heterogeneity, mobility and complexity of glycans in glycoproteins have been, currently remain, significant challenges structural biology. Those aspects present unique problems to the two most prolific techniques: X-ray crystallography cryo-electron microscopy. At same time, advances mass spectrometry made it possible get deeper insights on precisely information that is difficult recover by structure solution methods: full-length glycan composition, including linkage details for...