Institute of Molecular Function







   Last Modified

   23 February 2018

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Homology Modeling Professional for HyperChem


Estimation of Hydrogen Atoms in Water



In a protein crystal structure, all hydrogen atoms are coordinated to a certain direction due to lower resolutions of the electron density. The hydrogen atoms of both amino acid residues and small molecules in a protein crystal structure can be automatically attached to the heavy atoms using molecular mechanics calculations through mapping to the observed electron density map. In contrast, none of the hydrogen atoms of water molecules in the protein crystal structure are considered due to the large number of molecules and the less information. However, the hydrogen atoms of the water molecules are strongly involved in the determination of electrostatic potentials on the protein surface and that of dielectric constant, as well as are an important factor contributing to the hydrogen bond network in the ligand binding site. The "Estimation of Hydrogen Atoms in Water" program can automatically and logically prepare an reliable initial structure of a hydrogen atom in a water molecule on the basis of an algorithm.


On an Importance of An Initial Structure in the Computational Chemistry

In the chemical calculations, an initial structure is the most important for obtaining a reliable structure, since the optimized structure strongly depends on the initial structure. The structure giving from the molecular dynamics calculations also depends on the initial structure, if the structure is not subjected to very long-time samplings at high temperature. Unfortunately, this can not be realized for a protein molecule system due to a large number of atoms. Thus, an algorithm which can prepare more reliable initial structure is necessary to treat a protein molecule system.




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