Enzyme Structure and Function

PDBrenum renumbers PDB files to align with UniProt sequences, resolving inconsistent amino acid numbering across PDB entries.

This paper improves macromolecular structure refinement using Phenix and OPLS3e for better structure and ligand quality in X-ray and cryo-EM data.

The paper introduces MCPdb, a database cataloging bacterial microcompartment structures and their assemblies, annotated for assembly state, structure, and metabolic function.

The paper presents structures of Arabidopsis thaliana PCOs and identifies key residues for N-Cys oxidation, revealing substrate recognition and catalytic mechanisms.

This paper models macromolecular atomic displacement parameters using a mixture of Shifted Inverse Gamma Distributions and introduces a local analysis method for detecting structural errors.

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.

The paper develops a method to convert electron density maps into units of electrons, enabling biochemical interpretation of structural quality in PDB entries.

The paper determines crystal structures of SARS-CoV-2 ADRP and shows conformational changes upon ligand binding, identifying a conserved water molecule involved in hydrolysis.

The paper identifies an iron-dependent enzyme in plants that completes the lysine catabolism pathway, showing structural and functional conservation across species.

The paper introduces an automated pipeline for SAXS data analysis of transmembrane proteins in detergent solutions, improving model resolution with a priori information.

The paper presents a deep learning algorithm using an auto-encoder to reconstruct 3D protein models from SAXS data, demonstrating accuracy without prior size information.

This paper introduces an ab-initio method to derive 3D protein structures from SAXS data and primary sequences, validated using crystal structures and showing success in modeling a coiled-coil protein.

The paper refines a protein structure using quantum chemistry restraints, incorporating crystallographic symmetry effects through a fragmentation approach.

The paper integrates the Amber force field into Phenix for crystallographic refinement, improving model quality through better stereochemistry, fewer clashes, and better hydrogen bonds.

The paper identifies high-quality metal ion-centric regions in the wwPDB by evaluating structural quality using electron density maps and four quality criteria.

The paper analyzes biological assemblies in protein structures, highlighting challenges in determining correct assemblies and recent computational methods that use interface similarity.

The paper introduces a web server for predicting crystallization success of transmembrane proteins using a method tailored for membrane proteins.

The paper reports the 2.08 Å resolution structure of HLB5, a novel cellulase from Parabacteroides johnsonii, which lacks structural homologues or conserved regions typical of carbohydrate-degrading enzymes.

ProtMiscuity is a manually-curated database of promiscuous proteins containing 57 proteins from 40 organisms with 88 reactions, providing annotated data linked to other resources.

pdb-tools provides command-line Python scripts for editing, converting, and validating PDB files without external dependencies.

This paper demonstrates a wheat-germ cell-free protein expression pipeline that generates high-purity proteins for structural biology analysis.

The paper presents methods to complete missing regions in protein structures using homology information, resulting in 24,962 completed loops in the PDB.

The paper describes real-space refinement in Phenix for improving cryo-EM models using additional restraints and shows significant model improvement.

The paper presents a method to assess the quaternary structure of proteins from crystal data by combining interface classification with symmetry and topology analysis, achieving 85% precision on a new dataset.

The paper describes improvements to the automatic characterization and data collection algorithms on the MASSIF-1 beamline, enhancing data quality and throughput.

The paper introduces MMTF, a new binary format for macromolecular structures, which is faster and smaller than PDBx/mmCIF, enabling efficient visualization and analysis.

The paper characterizes the alanine racemase from Streptomyces coelicolor, showing its essential role in D-Ala production and sensitivity to D-cycloserine.