Amide I Vibrational Spectroscopy Lab

By Michael Earl Reppert1; Jacob Hnatusko Wat1

1. Purdue University

This tool allows users to upload/fetch protein databank files, visualize the protein structure, and calculate Amide I vibrational spectra for the protein.

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Version 1.4 - published on 17 Nov 2022

doi:10.21981/9Y77-RJ87 cite this

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Abstract

AmideSpec provides an interface for calculating Amide I (backbone carbonyl stretch) vibrational spectra. The user can upload a *.pdb file or fetch one from the RCSB Protein Data Bank (http://www.rcsb.org/). A simple interface for visualizing the loaded structure is provided. The user can then calculate inter-site couplings between amide groups using the point-dipole coupling model of Torii and Tasumi [J Raman Spec., VOL. 29, 81-86 (1998)] and simulate the FTIR spectrum under the assumption that all vibrational groups have a uniform frequency of 1650 cm-1. 

The app is currently undergoing testing and is advised only for educational (not research) purposes. Future versions of the interface are planned to allow for structure-based site energy estimation, molecular dynamics simulations, and two-dimensional (2D) infrared (IR) spectral simulations. 

Version 1.3 (installed Nov 16, 2022) fixed a bug in which nearest-neighbor couplings were incorrectly set to zero.

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Cite this work

Researchers should cite this work as follows:

  • Michael Earl Reppert, Jacob Hnatusko Wat (2022), "Amide I Vibrational Spectroscopy Lab," https://nanohub.org/resources/amidespec. (DOI: 10.21981/9Y77-RJ87).

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Tags

  1. AFM-IR spectroscopy
  2. Amide I
  3. FTIR
  4. nano/bio
  5. Protein