Weichenberger C.X.,K.k. Hofkristallamt |
Pozharski E.,University of Maryland, Baltimore |
Rupp B.,K.k. Hofkristallamt |
Rupp B.,Innsbruck Medical University
Acta Crystallographica Section D: Structural Biology | Year: 2017
The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallographic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein-peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electrondensity-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided.
PubMed | k.k. Hofkristallamt
Type: Journal Article | Journal: Postepy biochemii | Year: 2017
Biomolecular crystallography is a mature science that provides an instructive example for modern inductive reasoning as a model for Bayesian epistemology in empirical science. Fundamental scientific epistemology requires that a strong claim is supported by strong and convincing proof. Biomolecular crystallography, based on solid foundations of rich experimental data and extensive prior knowledge provides a prime example for modern, evidence based reasoning that strongly relies on assessments of plausibility based on prior knowledge while at the same time constantly delivering some of the most novel and exciting results based on new experimental evidence. As a consequence of the solid underlying physical principles and its mathematical rigor, crystallography as a mature science could be almost fool proof - were it not for the human element.