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1.
Nucleic Acids Res ; 2024 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-39162213

RESUMO

Nucleic acid electron density interpretation after phasing by molecular replacement or other methods remains a difficult problem for computer programs to deal with. Programs tend to rely on time-consuming and computationally exhaustive searches to recognise characteristic features. We present NucleoFind, a deep-learning-based approach to interpreting and segmenting electron density. Using an electron density map from X-ray crystallography obtained after molecular replacement, the positions of the phosphate group, sugar ring and nitrogenous base group can be predicted with high accuracy. On average, 78% of phosphate atoms, 85% of sugar atoms and 83% of base atoms are positioned in predicted density after giving NucleoFind maps produced following successful molecular replacement. NucleoFind can use the wealth of context these predicted maps provide to build more accurate and complete nucleic acid models automatically.

2.
Beilstein J Org Chem ; 20: 931-939, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38711584

RESUMO

The remediation of the carbohydrate data of the Protein Data Bank (PDB) has brought numerous enhancements to the findability and interpretability of deposited glycan structures, yet crucial quality indicators are either missing or hard to find on the PDB pages. Without a way to access wider glycochemical context, problematic structures may be taken as fact by keen but inexperienced scientists. The Privateer software is a validation and analysis tool that provides access to a number of metrics and links to external experimental resources, allowing users to evaluate structures using carbohydrate-specific methods. Here, we present the Privateer database, a free resource that aims to complement the growing glycan content of the PDB.

3.
Acta Crystallogr F Struct Biol Commun ; 80(Pt 2): 30-35, 2024 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-38265073

RESUMO

Owing to the difficulties associated with working with carbohydrates, validating glycan 3D structures prior to deposition into the Protein Data Bank has become a staple of the structure-solution pipeline. The Privateer software provides integrative methods for the validation, analysis, refinement and graphical representation of 3D atomic structures of glycans, both as ligands and as protein modifiers. While Privateer is free software, it requires users to install any of the structural biology software suites that support it or to build it from source code. Here, the Privateer web app is presented, which is always up to date and available to be used online (https://privateer.york.ac.uk) without installation. This self-updating tool, which runs locally on the user's machine, will allow structural biologists to simply and quickly analyse carbohydrate ligands and protein glycosylation from a web browser whilst retaining all confidential information on their devices.


Assuntos
Carboidratos , Aplicativos Móveis , Carboidratos/química , Cristalografia por Raios X , Glicosilação , Polissacarídeos/química
4.
Acta Crystallogr D Struct Biol ; 79(Pt 6): 462-472, 2023 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-37219590

RESUMO

The oligosaccharides in N-glycosylation provide key structural and functional contributions to a glycoprotein. These contributions are dependent on the composition and overall conformation of the glycans. The Privateer software allows structural biologists to evaluate and improve the atomic structures of carbohydrates, including N-glycans; this software has recently been extended to check glycan composition through the use of glycomics data. Here, a broadening of the scope of the software to analyse and validate the overall conformation of N-glycans is presented, focusing on a newly compiled set of glycosidic linkage torsional preferences harvested from a curated set of glycoprotein models.


Assuntos
Oligossacarídeos , Polissacarídeos , Polissacarídeos/química , Oligossacarídeos/química , Glicoproteínas/química , Glicosilação , Glicômica , Configuração de Carboidratos
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