ArticleThe journal of physical chemistry. B2011
Development and validation of transferable amide I vibrational frequency maps for peptides.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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67 citing papers in PubMed.
- Multidimensional Infrared Spectroscopy as a Bioanalytical Technique.Chemical reviews · 2026Review
- Molecular Dynamics-Instantaneous Frequencies of Molecules Method to Address the Performance of Classical and Rigid Water Force Fields.The journal of physical chemistry. B · 2026Article
- Machine learning potentials accurately reproduce vibrational dynamics in complex environments.The Journal of chemical physics · 2025Article
- A machine learning protocol for predicting structural distributions of amyloid-forming proteins from 2D IR spectra.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- IR Spectroscopy: From Experimental Spectra to High-Resolution Structural Analysis by Integrating Simulations and Machine Learning.The journal of physical chemistry. B · 2025Article
- Beyond Electrostatic Interactions: H-Bond Dynamics in Arginine- versus Lysine-Rich Biocondensates.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
- Do selectivity filter carbonyls in KJournal of structural biology: X · 2024Article
- Estimation of vibrational spectra of Trp-cage protein from nonequilibrium metadynamics simulations.Biophysical journal · 2024Article
- Salivary Molecular Spectroscopy with Machine Learning Algorithms for a Diagnostic Triage for Amelogenesis Imperfecta.International journal of molecular sciences · 2024Article
- Unraveling dynamic protein structures by two-dimensional infrared spectra with a pretrained machine learning model.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Water inside the Selectivity Filter of a KJournal of the American Chemical Society · 2024Article
- Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra.The journal of physical chemistry letters · 2023Article
- Universal machine learning for the response of atomistic systems to external fields.Nature communications · 2023Article
- Probing Ion Configurations in the KcsA Selectivity Filter with Single-Isotope Labels and 2D IR Spectroscopy.Journal of the American Chemical Society · 2023Article
- Unpolarized laser method for infrared spectrum calculation of amide I CO bonds in proteins using molecular dynamics simulation.Computers in biology and medicine · 2023Article
- Design of an Electrostatic Frequency Map for the NH Stretch of the Protein Backbone and Application to Chiral Sum Frequency Generation Spectroscopy.The journal of physical chemistry. B · 2023Article
- AIM: A Mapping Program for Infrared Spectroscopy of Proteins.Journal of chemical theory and computation · 2022Article
- AI-based spectroscopic monitoring of real-time interactions between SARS-CoV-2 and human ACE2.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Vibrational exciton delocalization precludes the use of infrared intensities as proxies for surfactant accumulation on aqueous surfaces.Chemical science · 2021Article
7 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
Infrared (IR) spectroscopy of the amide I band has been widely utilized for the analysis of peptides and proteins. Theoretical modeling of IR spectra of proteins requires an accurate and efficient description of the amide I frequencies. In this paper, amide I frequency maps for protein backbone and side chain groups are developed from experimental spectra and vibrational lifetimes of N-methylacetamide and acetamide in different solvents. The frequency maps, along with established nearest-neighbor frequency shift and coupling schemes, are then applied to a variety of peptides in aqueous solution and reproduce experimental spectra well. The frequency maps are designed to be transferable to different environments; therefore, they can be used for heterogeneous systems, such as membrane proteins.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.