MOLECULAR DYNAMICS ANALYSIS TOOLS FOR COLLAGEN

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Molecular dynamics studies of the structure of collagen peptides yields a large volume of data that need to be examined for specific properties such as helical parameters, average dihedral angles, hydrogen bonding patterns. A number of tools have been developed to filter the data to present specific properties in a semi-automated fashion. Output of tools include averages and standard deviations of angles, radial and Cartesian time plots of dihedral angles and linear time plots of hydrogen bond geometries. In preparation for publication, a number of new tools were developed to generate plots. Two MidasPlus delegates were written to facilitate the analysis of solvent distribution about collagen during molecular dynamics simulation.