Hydropathy can be loosely defined as including both the hydrophobic and polar properties of molecules.  It is empirical, generally derived from experimental partition coefficients of small molecules between two solvents (usually 1-octanol and water).  Hydropathy encodes a pervasive force in Nature and in biological structure � leading to protein folding, ligand binding and other effects.  Importantly, entropy-driven effects are not acounted for with Newtonian mechanics simulations .  Here we will describe results from three on-going projects that apply our HINT (Hydropathic INTeractions) approach in structural bioinformatics: 1) using  the HINT scoring function in X-ray structure refinement of low-resolution structures produces higher quality models than with conventional means; 2) hydropathic analysis of waters at protein-protein interfaces reveals several roles for water, including a surprising new motif - hydrophobic bubbles - waters trapped in hydrophobic environments; 3) analysis of the three-dimensional interaction environments of protein residues with hydropathic grid maps suggests a novel and revealing alternative to rotamer libraries.

Structural bioinformatics in 3D: Using hydropathic interactions for protein model building, analysis and prediction

243rd National Meeting (2012)

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