Inter-residue, inter-protein and inter-family coevolution: bridging the scales

Protein contacts, inter-residue interactions and side-chain modelling.

Three-dimensional structures of proteins are the support of their biological functions. Their folds are stabilized by contacts between residues. Inner protein contacts are generally described through direct atomic contacts, i.e. interactions between side-chain atoms, while contact prediction methods mainly used inter-Calpha distances. In this paper, we have analyzed the protein contacts on a re...

Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps.

In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the ...

Alley and inter-plot effect on chickpeas

Inter-residue interactions in membrane proteins

Knowing the precise 3D-structure of a protein is crucial to understand its functional mechanism at the molecular level and to develop new pharmacological agents to targeting it. Nowadays only a few hundred integral membrane protein structures have been solved at high resolution due to the associated technical difficulties. In the present study we aim to characterize the main interactions in alp...

Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions.

Whether knowledge-based intra-molecular inter-residue potentials are valid to represent inter-molecular interactions taking place at protein-protein interfaces has been questioned in several studies. Differences in the chain connectivity effect and in residue packing geometry between interfaces and single chain monomers have been pointed out as possible sources of distinct energetics for the tw...