It is observed that during divergent evolution of two proteins with a common phylogenetic origin, the structural similarity of their backbones is often preserved even when the sequence similarity between them decreases to a virtually undetectable level. Here we analyzed, whether the conservation of structure along evolution involves also the local atomic structures in the interfaces between sec...

One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work, we introduced AccuRefiner, a machine learning based tool for refining protein-protein complexes. Given a do...

Protein motions are a key feature to understand biological function. Recently, a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0.5 Å C-alpha root-mean-square-deviation (RMSD). To understand this distribution in terms of structure-function relationships, we studied a well curated and large dataset of ~5,000 proteins with experimen...

The goal of protein structural comparison attempts to establish an equivalence relation between polymer structures based on their shapes and threedimensional conformations. Root mean square deviation (RMSD), a frequently-used approach, measures the average distance between the selected atoms of superimposed proteins. Although the RMSD is most popularly implemented, it suffers from a few drawbac...

The NMR protein structures are often deposited in the Protein Data Bank as ensembles of models that agree with the experimental restraints. Information about stereochemical variability and the molecular flexibility can be obtained by systematic comparison of all models. Here we describe CARON, a software that allows the computation of the root-mean-square-distances between equivalent atoms and ...

In this article, statistical properties of the root mean square deviation (RMSD) item fit statistic in response models are studied. It is shown that RMSD estimates will indicate even misfit for items whose parametric assumption function correct (i.e., fitting items) if some functions test misspecified. Moreover, it demonstrated values misfitting and depend on proportion items. We propose three ...