Stephen Kevin Burley

OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway

This study identifies OSTM1 as a tumor suppressor in B-cell malignancies by showing it activates the cAMP/PKA/CREB pathway through ubiquitin E3 ligase activity.

The NMR Exchange Format (NEF): Specification and Applications

The paper introduces NEF, a standard for NMR data exchange, and demonstrates its application in structure determination, metabolomics, and ligand screening.

Multi-scale structural similarity embedding search across entire proteomes

This paper introduces a scalable method for searching 3D protein structure similarity across entire proteomes using deep learning and vector databases.

Q-score as a reliability measure for protein, nucleic acid, and small molecule atomic coordinate models derived from 3DEM density maps

The paper introduces and analyzes Q-scores to assess the reliability of atomic coordinate models fitted to 3DEM maps, showing their correlation with map resolution and model quality.

An AI/ML-modeled structural atlas of the human protein interactome with functional and cancer-focused networks

The paper uses Boltz-2 to predict structural models of human protein interactions and identifies functional and cancer-related networks.

High-throughput prediction of peptide structural conformations with AlphaFold2

This study evaluates AlphaFold2's ability to predict peptide structural conformations using NMR data, finding varying accuracy with RMSD under 2.5 Å and RMSF under 1.5 Å.

Generative artificial intelligence performs rudimentary structural biology modeling

This study shows that GPT-4 can generate 3D protein structures and analyze ligand-protein interactions with atomic-scale accuracy, though it has limitations with complex models.

Restraint Validation of Biomolecular Structures Determined by NMR in the Protein Data Bank

The paper develops a standardized system for validating biomolecular structures against NMR restraints using NEF and NMR-STAR formats, implemented in the wwPDB OneDep system.

PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank

The PDB NextGen Archive centralizes and streamlines access to integrated structural annotations and enriched data from wwPDB partners and external sources.

EMDB - The Electron Microscopy Data Bank

The paper provides an overview of the EMDB archive, its current holdings, recent updates, and future plans.

ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models

ModelCIF extends the PDBx/mmCIF standard to represent predicted 3D protein models, enabling FAIR data sharing for computational structural biology.

A comprehensive survey of coronaviral main protease active site diversity in 3D: Identifying and analyzing drug discovery targets in search of broad specificity inhibitors for the next coronavirus pandemic

The paper analyzes the diversity of coronaviral main protease active sites to identify potential broad-spectrum inhibitors for future pandemics.

Real-time structural motif searching in proteins using an inverted index strategy

The paper introduces an inverted index method for real-time structural motif searching in the PDB, enabling efficient analysis of 3D protein and nucleic acid structures.

Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic

The paper analyzes 3D structural changes in SARS-CoV-2 proteins during the first six months of the pandemic, showing amino acid substitutions primarily affect surfaces and boundary layers.

Real time structural search of the Protein Data Bank

The paper introduces a method for real-time retrieval of protein structures from the PDB by comparing electron density volumes using 3D Zernike moments.

Quaternary structure evaluation tool for protein assemblies

The paper evaluates quaternary structure annotations in the PDB by comparing prediction methods and develops a web tool for researchers.