Enzyme Structure and Function

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

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

Finding high-quality metal ion-centric regions across the worldwide Protein Data Bank

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

iCn3D, a Web-based 3D Viewer for Sharing 1D/2D/3D Representations of Biomolecular Structures

An anticipated optimization approach to macromolecular crystallization

The paper introduces an anticipated optimization approach to improve crystallization yield for challenging protein samples, showing increased success in producing useful crystals.

Parsers, Data Structures and Algorithms for Macromolecular Analysis Toolkit (MAT): Design and Implementation

The paper introduces MAT, a toolkit for parsing and analyzing macromolecular data files, offering faster and more accurate parsing with new data structures and algorithms.

Principles and characteristics of biological assemblies in experimentally determined protein structures

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

The TMCrys server for supporting crystallization of transmembrane proteins

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

A 2.08 A resolution structure of HLB5, a novel cellulase from the anaerobic gut bacterium Parabacteroides johnsonii DSM 18315.

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: a database of promiscuous proteins

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: a swiss army knife for molecular structures

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

Protein Structural Biology Using Cell-Free Platform from Wheat Germ

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

Homology-based loop modelling yields more complete crystallographic protein structures

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

Z-score to evaluate the absolute quality of macromolecular models based on SAXS data

The paper introduces a Z-score metric to evaluate the quality of SAXS-based macromolecular models by assessing their ability to differentiate between possible structures.

Real-space refinement in Phenix for cryo-EM and crystallography

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

Automated evaluation of quaternary structures from protein crystals

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.

Recent improvements to the automatic characterization and data collection algorithms on MASSIF-1

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

Quaternary structure evaluation tool for protein assemblies

The paper evaluates quaternary structure annotations in the PDB by comparing prediction methods and develops a web tool for researchers.

MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures

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

Structural and Functional Characterization of the Alanine Racemase from Streptomyces coelicolor A3(2)

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