A new methodology that combines the generalized topological indices (GTI) and the down hill simplex optimisation procedure has been developed to search for optimised quantitative structure–property relationship models. The structural interpretation of the optimal molecular descriptors is attained analytically by means of the GTIs decomposition in terms of geodesics (shortest paths) in the molec...

Construction and physico-chemical behavior of DNA three way junction (3WJ) functionalized by protein-like residues (imidazole, alcohol and carboxylic acid) at unpaired positions at the core is described. One 5′-C(S)-propargyl-thymidine nucleotide was specifically incorporated on each strand to react through a post synthetic CuACC reaction with either protected imidazolyl-, hydroxylor carboxyl-a...

The topographical and physico-chemical complexity of protein-water interfaces scales down to the sub-nanoscale range. At this level of confinement, we demonstrate that the dielectric structure of interfacial water entails a breakdown of the Debye ansatz that postulates the alignment of polarization with the protein electrostatic field. The tendencies to promote anomalous polarization are determ...

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...

Late Embryogenesis Abundant proteins (LEAPs) comprise several diverse protein families and are mostly involved in stress tolerance. Most of LEAPs are intrinsically disordered and thus poorly functionally characterized. LEAPs have been classified and a large number of their physico-chemical properties have been statistically analyzed. LEAPs were previously proposed to be a subset of a very wide ...

Active sites in proteins are three dimensional substructures that cause them to perform their function. The problem of finding substructures in a protein that are “similar” to the active sites of another protein has several important applications in biological sciences such as drug design, genetic engineering, and diagnostic tools for analysis of genetically engineered pathogens. Active sites c...