Grzegorz Chojnowski

A validation approach for RNA structures based on deep-learning 3D-structure predictions

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

Single-site DNA methylation activates retron defence by enabling effector tetramerisation

This study shows that single-site DNA methylation activates Retron-Sen2 by enabling RcaT tetramerisation, leading to retron disassembly and toxicity.

Intrinsic flexibility of Type VII secretion central pore is required for substrate translocation

This study shows that the flexibility of the central pore in the ESX-5 type VII secretion system is essential for efficient substrate translocation, as rigidification of key residues impairs secretion.

gapTrick - Structural characterisation of protein-protein interactions using AlphaFold

The paper introduces gapTrick, an AlphaFold2-based method that improves prediction of weak and incomplete protein complexes using multimeric templates.

Structure of Pex8 in complex with peroxisomal receptor Pex5 reveals its essential role in peroxisomal cargo translocation

This study reveals the structural and functional role of Pex8 in peroxisomal cargo translocation by interacting with Pex5, facilitating receptor recycling.

AlphaPulldown2 - A General Pipeline for High-Throughput Structural Modeling

AlphaPulldown2 provides a pipeline for high-throughput protein structural modeling with automated workflows and improved data management.

Using deep learning predictions reveals a large number of register errors in PDB deposits

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

Master corepressor inactivation through multivalent SLiM-induced polymerization mediated by the oncogene suppressor RAI2

The paper shows RAI2 induces CtBP polymerization, leading to loss of corepressor function in cancer cells and reduced RAI2 in advanced prostate cancer.

RNA fragment assembly with experimental restraints

RNA Masonry assembles RNA fragments into geometrically plausible models using secondary structure constraints and SAXS data.

doubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models

doubleHelix identifies and validates nucleic acid sequences in cryo-EM and crystal structures, improving accuracy at lower resolutions and detecting errors missed by existing methods.

Sequence assignment validation in protein crystal structure models with checkMySequence

The paper validates sequence assignment in protein crystal structure models using an automated method called checkMySequence, identifying register shift errors in PDB-deposited models.

Asymmetric horseshoe-like assembly of peroxisomal Yeast Oxalyl-CoA synthetase

The paper determines the structural assembly of yeast Oxalyl-CoA synthetase, revealing asymmetric hexameric arrangements and identifying key self-association interfaces.

AlphaPulldown - a Python package for protein-protein interaction screens using AlphaFold-Multimer

AlphaPulldown is a Python package that simplifies protein-protein interaction screens and high-throughput modelling using AlphaFold-Multimer, offering a CLI, confidence scores, and a graphical tool.

Using deep learning predictions of inter-residue distances for model validation

The paper introduces validation methods using deep learning-predicted inter-residue distances to detect and correct sequence register errors in protein models.

Sequence assignment validation in cryo-EM models with checkMySequence

The paper introduces checkMySequence, an automated method to detect register-shift errors in cryo-EM protein models, improving accuracy in cases of low map resolution.

Identification of unknown proteins in X-ray crystallography and cryo-EM

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.