Jennifer R. Fleming

PDBe-SIFTS improves residue-level sequence-structure mapping with faster search, better scoring, and accurate alignment, comparable to expert curation.

The paper predicts quaternary structures of viral proteins using AlphaFold2 and AlphaFold-Multimer, identifying new insights into vaccinology and protease targets.

A parallelized BindCraft pipeline generated 306,146 in silico binder candidates against 8,296 human proteins, each with sequence, predicted complex and confidence metrics, freely accessible online.

The paper expands the AlphaFold Protein Structure Database to include proteome-scale quaternary structures, predicting 1.81M high-confidence protein complexes and revealing conserved structural clusters across domains of life.

This study introduces ECIFP, a method to analyze ligand binding modes in the PDB, showing it can identify similar binding sites and detect binding-mode similarities across diverse ligands.

This study identifies CtdA, a tRNA deacetylase that removes canavanine from mischarged tRNAArg, and reveals its structural and evolutionary relationships to B3/B4 domains.

The paper introduces PDBe tools for analysing small molecules in the PDB, enhancing ligand data access, interaction analysis, and functional role identification.

The paper introduces a protocol for using PaSiMap within Jalview to analyze protein-sequence relationships and provides an R script for data visualization.

PaSiMap is a multidimensional scaling tool for classifying protein sequences, revealing hierarchical Ig domain similarities and a previously unidentified repeat in titin.