We propose a method for comparing protein structures or, more specifically, protein binding sites using a histogram-based representation that captures important geometrical and physico-chemical properties. In comparison to hitherto existing approaches in structural bioinformatics, especially methods from graph theory and computational geometry, our approach is computationally much more efficien...

Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms 2 io 6

UNLABELLED The reliable assessment of the quality of protein structural models is fundamental to the progress of structural bioinformatics. The ModFOLD server provides access to two accurate techniques for the global and local prediction of the quality of 3D models of proteins. Firstly ModFOLD, which is a fast Model Quality Assessment Program (MQAP) used for the global assessment of either sing...

Intrinsically disordered proteins a nd c omplex multidomain proteins are characterized by dynamic ensembles of conformations that cannot be unequivocally de scribed by t raditional s tatic te rms o f s tructural b iology. These states of proteins are critical in understanding their function at the atomic level, which will eventually lead to extending the structure-function paradigm to establish...

Developing a drug de novo is a laborious and costly endeavor. Thus, the repositioning of already approved drugs for the treatment of new diseases is promising and valuable. One computational approach to repositioning exploits the structural similarity of binding sites of known and new targets. Here, we review computational methods to represent and align binding sites. We review available tools,...