Alex G. Bateman

Large-scale structure prediction of DUF-containing protein-protein interactions

A logistic regression on STRING evidence picked DUF (domain of unknown function) protein pairs for AlphaFold 3; of 12,298 modelled pairs, 1,208 met strict and 2,433 liberal confidence.

Structural basis of biofilm formation mediated by the Pseudomonas aeruginosa fibrillar adhesin CdrA

This study determines the structure of CdrA, a fibrillar adhesin in Pseudomonas aeruginosa, revealing its role in biofilm formation and identifying targets for inhibition.

Viral non-coding RNA structure annotation and API-based data retrieval with Rfam and R2DT

The paper describes methods for automated viral ncRNA annotation and programmatic access to Rfam data via its API, enabling integration into bioinformatics workflows.

Folding the unfoldable 2: using AlphaFold and ESMFold to explore spurious proteins

The paper evaluates if newer structure prediction methods can better distinguish spurious proteins from real ones, finding improved discrimination beyond 100 amino acids.

GOFlowLLM - Curating miRNA literature with Large Language Models and flowcharts

GOFlowLLM automates miRNA literature curation using LLMs and flowcharts, achieving high accuracy and efficiency in annotating gene silencing data.

Isopeptor: a tool for detecting intramolecular isopeptide bonds in protein structures

Isopeptor detects intramolecular isopeptide bonds in protein structures using structure-guided template matching and logistic regression, achieving high recall and precision on a curated PDB subset.

Rfam 15: RNA families database in 2025

Rfam 15.0 expands coverage to 26,106 genomes, improves RNA family annotations with 3D structures, and synchronizes with miRBase, enhancing RNA research and machine learning applications.

Annotation of biologically relevant ligands in UniProtKB using ChEBI

The paper reannotates ligand binding sites in UniProtKB using ChEBI identifiers and improves search facilities for these annotations.

Expanding the repertoire of human tandem repeat RNA-binding proteins

The paper identifies 219 human tandem repeat proteins that bind RNA using sequence and structural methods, showing their combined effectiveness over individual approaches.

Large Scale Discovery of Microbial Fibrillar Adhesins and Identification of Novel Members of Adhesive Domain Families

The paper develops a random forest method to identify fibrillar adhesins in bacterial proteomes, discovering over 6,500 candidates and 24 novel adhesive domain families.

Using Deep Learning to Annotate the Protein Universe

This paper uses deep learning to improve protein function annotation by training on Pfam data, achieving better accuracy and efficiency than BLASTp.

Reciprocal Best Structure Hits: Using AlphaFold models to discover distant homologues

This paper uses AlphaFold 2.0 structure models to detect homologous protein pairs, finding similar results to sequence-based methods and identifying novel homologues.

Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states

The paper presents cryo-EM structures of human RNA polymerase III in unbound and transcribing states, revealing structural insights into its function and disease associations.

Caenorhabditis elegans AF4/FMR2 family homolog affl-2 is required for heat shock induced gene expression

This study identifies affl-2, a C. elegans ortholog of the human AF4/FMR2 family, as a regulator of heat shock induced gene expression.

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

The paper assesses the value and sustainability of ELIXIR Core Data Resources, showing their critical role in preserving biological data and highlighting funding challenges.

The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest

The paper introduces XRNAX, a method to purify protein-RNA complexes, and shows it captures all RNA biotypes and reveals dynamic changes in the RNA-bound proteome during arsenite-induced stress.

On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study

The paper assesses the sustainability of expert curation in UniProtKB/Swiss-Prot by analyzing literature triage and curatorial workload.