Sensitivity of protein - Ligand interaction energies with respect to spatial positions of hydrogen atoms

The development in many fields of biological and biochemical researches depends on researching values of chemical affinities between chemical molecules (ligands), and active sites of proteins. Results of those researches are applicable e.g. in the design of new drugs or studying mechanisms of progression of some diseases. Due to a very wide area of potential applications the methods for computational prediction of interactions between proteins and ligands are developing at a fast rate. The algorithms need constant tuning and refining to trace the constant inflow of new experimental data. In this talk we present the study on the sensitivity of protein - ligand interaction energies with respect to spatial positions of hydrogen atoms. The affinities between protein active sites and ligand molecules are mostly resulting from the hydrogen bonds. However, spatial positions of hydrogen atoms are often not obvious. By using different methods we can obtain different estimates of positions of hydrogen atoms. This pursued us to conduct a study on the sensitivity of ligand - protein bond energies on positions of hydrogen atoms. We used the published algorithm for correcting positions of the hydrogen atoms in asparagines, glutamines and histidines to compute corrections in binding pockets in 556 molecular complexes. Using this data we have computed the corresponding corrections in the bonding energies. We show the obtained result using our system for analysis of interaction of molecular ligand-protein complexes based on the Matlab environment.