Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank

By Robbie P. Joosten, Krista Joosten, Serge X. Cohen, G. Vriend, Anastassis Perrakis. 2011

93 citations recorded by the source corpus.

Motivation: Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. With PDB_REDO, we aim to automatically optimize these structures to better fit their corresponding experimental data, passing the benefits of new methods in crystallography on to a wide base of non-crystallographer structure users. Results: We developed new algorithms to allow automatic rebuilding and remodeling of main chain peptide bonds and side chains in crystallographic electron density maps, and incorporated these and further enhancements in the PDB_REDO procedure. Applying the updated PDB_REDO to the oldest, but also to some of the newest models in the PDB, corrects existing modeling errors and brings these models to a higher quality, as judged by standard validation methods. Availability and Implementation: The PDB_REDO database and links to all software are available at http://www.cmbi.ru.nl/pdb_redo. Contact: r.joosten@nki.nl; a.perrakis@nki.nl Supplementary Information: Supplementary data are available at Bioinformatics online.

Subfields: Materials Chemistry, Molecular Biology, Structural Biology

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Citations in the corpus

PDB_REDO: constructive validation, more than just looking for errors (2012, methodology): “(ii) The program pepflip (Joosten, Joosten et al., 2011) is used to flip the orientation of peptide planes in the model if this improves the fit of the peptide with, in order of importance, the mFo DFc map at the position of the oxygen, the 2mFo DFc map of the whole peptide and a combination of the…”
A series of PDB-related databanks for everyday needs (2014, background): “00 or newer which means that all structure models have undergone rebuilding of side chains and flipping of peptide plane orientations when needed (52).”
The PDB_REDO server for macromolecular structure model optimization (2014, background): “…[which (re)builds side chains in rotameric conformations] and pepflip (which flips the orientation of peptide planes to improve the fit with electron-density maps and the Ramachandran plot; Ramachandran et al., 1963) (Joosten et al., 2011), and validation in WHAT_CHECK (Hooft et al., 1996).”
MolProbity’s Ultimate Rotamer-Library Distributions for Model Validation (2016, unknown): “…these libraries form the conformational criteria used in a variety of applications including crystallographic model building and refinement,8,13 protein structure prediction and design,14–16 and protein model validation.17 –19 Different rotamer libraries represent the allowed variability…”