Adam J. Simpkin

This paper extends a protein structure validation method to RNA, showing it can detect errors in low-resolution structures where map-based methods fail.

reactifpTM reimplements actifpTM to calculate interface quality scores using standard outputs from model prediction software, showing strong correlation with actifpTM on a PDB dataset.

The paper presents high-resolution structures of Helicobacter pylori TlpD, revealing how ligand-binding perturbations propagate through coiled-coils to regulate kinase interfaces.

This paper evaluates AlphaFold 3 and other methods in predicting α-synuclein polymorphs using a reference set of known structures and finds they can generate fibril-like models, though performance varies with template use.

This study investigates the role of Akkermansia muciniphila sulfatases in colonic mucin utilization, revealing unique adaptations compared to Bacteroides species.

The paper evaluates AlphaFold 2's performance on repeat proteins, finding it predicts confident but unrealistic beta-solenoid structures, unlike other methods.

ABCFold simplifies running and comparing AlphaFold 3, Boltz-1, and Chai-1 for protein structure prediction with standardized input and unified result handling.

The paper assesses how many protein structures still require experimental phasing when using AlphaFold 2 models, finding that most can be solved with Molecular Replacement.

The paper identifies thousands of register errors in PDB structures using deep learning predictions and shows corrections improve refinement statistics.

The paper uses AlphaFold2 to predict structures of three uncharacterized apicoplast proteins and suggests their potential molecular functions as transporters.

The paper uses deep learning to predict structures and functions of hypothetical proteins in Pandoraviruses, identifying some functional roles but finding many remain unclear.

This study uses computational structural biology to reveal the topology and function of Oca2, showing it is a Na+/dicarboxylate symporter with a unique structure and potential role in melanosomal trafficking.

SliceNDice improves Molecular Replacement by splitting and repositioning predicted structural models to enhance accuracy in domain orientations.

MrParse streamlines Molecular Replacement by consolidating homologue searches and rankings from PDB and EBI AlphaFold, using eLLG and structural predictions.

The paper presents an automated pipeline to identify protein sequences from cryo-EM and crystallographic data, demonstrating its application on an unknown snake venom protein.

This paper evaluates CASP14 models for molecular replacement using a new metric, reLLG, which is independent of diffraction data and shows AlphaFold2 models outperform others.

This paper introduces helical ensembles as improved search models for molecular replacement, achieving a 30% increase in solutions and faster convergence compared to ideal helices.