AIM: A Mapping Program for Infrared Spectroscopy of Proteins
Journal of Chemical Theory and Computation, 2022, Volume 18, pp. 3089-3098.
Here, we present a new analysis program, AIM, that allows extracting thevibrational amide-I Hamiltonian using molecular dynamics trajectories for protein infraredspectroscopy modeling. The constructed Hamiltonians can be used as input for spectralcalculations allowing the calculation of infrared absorption spectra, vibrational circulardichroism, and two-dimensional infrared spectra. These spectroscopies allow the study of thestructure and dynamics of proteins. We will explain the essence of how AIM works and give examples of the information and spectra that can be obtained with the program using theTrypsin Inhibitor as an example. AIM is freely available from GitHub, and the packagecontains a demonstration allowing easy introduction to the use of the program.
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