A5091516295- Enzyme Structure and Function
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Advancements in Photolithography Techniques
- RNA modifications and cancer
- Machine Learning in Materials Science
- Advanced Electron Microscopy Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Glycosylation and Glycoproteins Research
- Advancements in Semiconductor Devices and Circuit Design
- Bacteriophages and microbial interactions
- Computational Drug Discovery Methods
- Mass Spectrometry Techniques and Applications
- NMR spectroscopy and applications
- Carbohydrate Chemistry and Synthesis
- Business Process Modeling and Analysis
- Plant Molecular Biology Research
- Genomics and Phylogenetic Studies
- ATP Synthase and ATPases Research
- Software Engineering and Design Patterns
- Enzyme Production and Characterization
- Bioinformatics and Genomic Networks
- Ubiquitin and proteasome pathways
- Cancer-related molecular mechanisms research
University of York
2023-2025
Diamond Light Source
2020-2024
University of Liverpool
2019-2024
University of Helsinki
2019
Didcot Community Hospital
2019
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...
The results of tertiary structure assessment at CASP15 are reported. For the first time, recognizing outstanding performance AlphaFold 2 (AF2) CASP14, all single-chain predictions were assessed together, irrespective whether a template was available. At CASP15, there no single stand-out group, with most best-scoring groups-led by PEZYFoldings, UM-TBM, and Yang Server-employing AF2 in one way or another. Many top groups paid special attention to generating deep Multiple Sequence Alignments...
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...
With the advent of next-generation modelling methods, such as AlphaFold 2, structural biologists are increasingly using predicted structures to obtain structure solutions via molecular replacement (MR) or model fitting in single-particle cryogenic sample electron microscopy (cryoEM). Differences between domain–domain orientations represented a and crystal often key limitation when models. Slice'N'Dice is software package designed address this issue by first slicing models into distinct units...
We report here an assessment of the model refinement category 14th round Critical Assessment Structure Prediction (CASP14). As before, predictors submitted up to five ranked refinements, along with associated residue-level error estimates, for targets that had a wide range starting quality. The ability groups accurately rank their submissions and predict coordinate varied widely. Overall, only four out-performed "naïve predictor" corresponding resubmission model. Among top groups, there are...
In late 2020, the results of CASP14, 14th event in a series competitions to assess latest developments computational protein structure-prediction methodology, revealed giant leap forward that had been made by Google's Deepmind tackling prediction problem. The level accuracy their predictions was first instance competitor achieving global distance test score better than 90 across all categories difficulty. This achievement represents both challenge and an opportunity for field experimental...
The accuracy of the information in Protein Data Bank (PDB) is great importance for myriad downstream applications that make use protein structural information. Despite best efforts, occasional introduction errors inevitable, especially where experimental data are limited resolution. A novel structure validation approach based on spotting inconsistencies between residue contacts and distances observed a model those computationally predicted by methods such as AlphaFold2 has previously been...
Background: Recent strides in computational structural biology have opened up an opportunity to understand previously uncharacterised proteins. The under-representation of transmembrane proteins the Protein Data Bank highlights need apply new and advanced bioinformatics methods shed light on their structure function. This study focuses a family containing Pfam domain PF09335 ('SNARE_ASSOC'/ 'VTT '/'Tvp38'). One prominent member, Tmem41b, has been shown be involved early stages autophagosome...
Determination of protein structures typically entails building a model that satisfies the collected experimental observations and its deposition in Protein Data Bank. Experimental limitations can lead to unavoidable uncertainties during process building, which result introduction errors into deposited model. Many metrics are available for validation, but most limited consideration physico-chemical aspects or match data. The latest advances field deep learning have enabled increasingly...
The results of tertiary structure assessment at CASP15 are reported. For the first time, recognising outstanding performance AlphaFold 2 (AF2) CASP14, all single chain predictions were assessed together, irrespective whether a template was available. At there no stand-out group, with most best-scoring groups - led by PEZYFoldings, UM-TBM and Yang Server employing AF2 in one way or another. Many top paid special attention to generating deep Multiple Sequence Alignments (MSAs) testing variant...
<ns4:p><ns4:bold>Background:</ns4:bold> Recent strides in computational structural biology have opened up an opportunity to understand previously uncharacterised proteins. The under-representation of transmembrane proteins the Protein Data Bank highlights need apply new and advanced bioinformatics methods shed light on their structure function. This study focuses a family containing Pfam domain PF09335 ('SNARE_ASSOC'/ ‘VTT ‘/’Tvp38’/'DedA'). One prominent member, Tmem41b, has been shown be...
Covariance-based predictions of residue contacts and inter-residue distances are an increasingly popular data type in protein bioinformatics. Here we present ConPlot, a web-based application for convenient display analysis contact maps distograms. Integration predicted with other is often required to facilitate inference structural features. ConPlot can therefore use the empty space near map diagonal multiple coloured tracks representing sequence-based predictions. Popular file formats...
The conventional approach in molecular replacement is the use of a related structure as search model. However, this not always possible availability such structures can be scarce for poorly characterized families proteins. In these cases, alternative approaches explored, small ideal fragments that share high, albeit local, structural similarity with unknown protein. Earlier versions AMPLE enabled trialling library helices, which worked well largely helical proteins at suitable resolutions....
We report here an assessment of the model refinement category 14th round Critical Assessment Structure Prediction (CASP14). As before, predictors submitted up to five ranked refinements, along with associated residue-level error estimates, for targets that had a wide range starting quality. The ability groups accurately rank their submissions and predict coordinate varied widely. Overall only four out-performed “naïve predictor” corresponding resubmission model. Among top there are...
Abstract Malaria is a burdensome disease to humanity caused chiefly by the still poorly understood parasite genus Plasmodium . Much of pathogenic success these and other related parasites due presence apicoplast, comparatively characterised biosynthetic organelle containing many proteins unknown function. Here we present AlphaFold2 protein structure predictions together with further in silico analyses infer molecular functions for three uncharacterised transmembrane apicoplast PF3D7_0622700,...
The accuracy of the information in Protein Data Bank (PDB) is great importance for myriad downstream applications that make use protein structural information. Despite best efforts, occasional introduction errors inevitable, especially where experimental data are limited resolution. We have previously established a novel structure validation approach based on spotting inconsistencies between residue contacts and distances observed model those computationally predicted by methods such as...
Abstract Recent strides in computational structural biology have opened up an opportunity to understand previously mysterious uncharacterised proteins. The under-representation of transmembrane proteins the Protein Data Bank highlights need apply new and advanced bioinformatics methods shed light on their structure function. This study focuses such a family; containing Pfam domain PF09335 (‘SNARE_ASSOC’/‘VTT ‘/‘Tvp38’). One prominent member, Tmem41b, has been shown be involved early stages...
Abstract Determination of protein structures typically entails building a model that satisfies the collected experimental observations and its deposition in Protein Data Bank (PDB). Experimental limitations can lead to unavoidable uncertainties during process building, which result introduction errors into deposited model. Many metrics are available for validation, but most limited consideration physico-chemical aspects or match map. The latest advances field deep learning have enabled...
Abstract The conventional approach in molecular replacement (MR) is the use of a related structure as search model. However, this not always possible availability such structures can be scarce for poorly characterised families proteins. In these cases, alternative approaches explored, small ideal fragments that share high albeit local structural similarity with unknown protein. Earlier versions AMPLE enabled trialling library helices, which worked well largely helical proteins at suitable...
β-Galactosidases catalyse the hydrolysis of lactose into galactose and glucose; as an alternative reaction, some β-galactosidases also formation galactooligosaccharides by transglycosylation. Both reactions have industrial importance: is used to produce lactose-free milk, while been shown act prebiotics. For multi-domain β-galactosidases, hydrolysis/transglycosylation ratio can be modified truncation carbohydrate-binding modules. Here, analysis BbgIII, a multidomain β-galactosidase from...