ArticleJournal of chemical theory and computation2022
AIM: A Mapping Program for Infrared Spectroscopy of Proteins.
Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed.
- Machine learning potentials accurately reproduce vibrational dynamics in complex environments.The Journal of chemical physics · 2025Article
- IR Spectroscopy: From Experimental Spectra to High-Resolution Structural Analysis by Integrating Simulations and Machine Learning.The journal of physical chemistry. B · 2025Article
- Multiscale theoretical study of infrared spectroscopy for the thermal denaturation process of aprotinin.Journal of molecular modeling · 2025Article
- Beyond Electrostatic Interactions: H-Bond Dynamics in Arginine- versus Lysine-Rich Biocondensates.The journal of physical chemistry letters · 2025Article
- Membrane Interactions Drive Hydrogen-Bond Dynamics in the pH-Low Insertion Peptide (pHLIP).The journal of physical chemistry letters · 2025Article
- AI protocol for retrieving protein dynamic structures from two-dimensional infrared spectra.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Simultaneously Measured Kinetics of Two Amyloid Polymorphs Using Cross Peak Specific 2D IR Spectroscopy.The journal of physical chemistry letters · 2023Article
- Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra.The journal of physical chemistry letters · 2023Article
- Reconstructing the infrared spectrum of a peptide from representative conformers of the full canonical ensemble.Communications chemistry · 2023Article
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2 authors.
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Abstract
Here, we present a new analysis program, AIM, that allows extracting the vibrational amide-I Hamiltonian using molecular dynamics trajectories for protein infrared spectroscopy modeling. The constructed Hamiltonians can be used as input for spectral calculations allowing the calculation of infrared absorption spectra, vibrational circular dichroism, and two-dimensional infrared spectra. These spectroscopies allow the study of the structure 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 the Trypsin Inhibitor as an example. AIM is freely available from GitHub, and the package contains a demonstration allowing easy introduction to the use of the program.
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