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The three-dimensional architecture of biomolecules often creates specialized structural elements, notably short hydrogen bonds that have donor-acceptor separations below 2.7 Å. In this work, we statistically analyze 1663 high-resolution biomolecular structures from the Protein Data Bank and demonstrate that short hydrogen bonds are prevalent in proteins, protein-ligand complexes and nucleic acids. From these biological macromolecules, we characterize the preferred location, connectivity and amino acid composition in short hydrogen bonds and hydrogen bond networks, and assess their possible functional importance. Using electronic structure calculations, we further uncover how the interplay of the structural and chemical features determines the proton potential energy surfaces and proton sharing conditions in biological short hydrogen bonds.
Pubmed ID: 31588321
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Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects.
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