Homology-based loop modeling yields more complete crystallographic protein structures.

ABSTRACT: Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and 'graft' these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in the PDB-REDO pipeline has enabled the building of 24 962 missing loops in the PDB. The models and the automated procedures are publicly available through the PDB-RED

SUBMITTER: van Beusekom B 

PROVIDER: S-EPMC6126648 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature