Homology-based loop modelling yields more complete crystallographic protein structures

Abstract

AbstractInherent protein flexibility, poor or low-resolution diffraction data, or poor electron density maps, often inhibit building complete structural models during X-ray structure determination. However, advances in crystallographic refinement and model building nowadays often allow to complete previously missing parts. Here, we present 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 our PDB-REDO pipeline, allowed to build 24,962 missing loops in the PDB. The models and the automated procedures are publically available through the PDB-REDO databank and web server (https://pdb-redo.eu). More complete protein structure models enable a higher quality public archive, but also a better understanding of protein function, better comparison between homologous structures, and more complete data mining in structural bioinformatics projects.SynopsisThousands of missing regions in existing protein structure models are completed using new methods based on homology.