Homology-based loop modeling yields more complete crystallographic protein structures

IUCrJ
Bart van BeusekomAnastassis Perrakis

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-REDO databank and webserver. 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.

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Citations

Jan 8, 2020·Acta Crystallographica. Section D, Structural Biology·Min ZhengPavel V Afonine
Apr 17, 2019·Acta Crystallographica. Section D, Structural Biology·Bart van BeusekomRobbie P Joosten
Nov 6, 2018·Acta Crystallographica. Section F, Structural Biology Communications·Bart van BeusekomAnastassis Perrakis
Apr 26, 2020·Cellular and Molecular Life Sciences : CMLS·Haiyang WuNathalie Juge
Mar 7, 2020·Acta Crystallographica. Section D, Structural Biology·Grzegorz ChojnowskiVictor S Lamzin
Dec 3, 2020·Acta Crystallographica. Section D, Structural Biology·Lum WangMalgorzata Biczysko
Jan 7, 2021·Acta Crystallographica. Section D, Structural Biology·Bart van BeusekomRobbie P Joosten
Jun 26, 2021·Journal of Chemical Theory and Computation·Jia-Jie FengYun-Dong Wu
Sep 3, 2021·Acta Crystallographica. Section D, Structural Biology·Ida de VriesRobbie P Joosten
Nov 16, 2021·Protein Science : a Publication of the Protein Society·Christopher J WilliamsJane S Richardson

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Methods Mentioned

BETA
X-ray

Software Mentioned

SideAide
HODER
SEQATOMS
pepflip
Coot
Modelcompare
EDSTATS
clipper
PDB
REDO

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