Electrostatic frequency shifts in amide I vibrational spectra: Direct parameterization against experiment

Optimization of Model Parameters for Describing the Amide I Spectrum of a Large Set of Proteins

(2012) Eeva-Liisa Karjalainen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Parallel β-Sheet Vibrational Couplings Revealed by 2D IR Spectroscopy of an Isotopically Labeled Macrocycle: Quantitative Benchmark for the Interpretation of Amyloid and Protein Infrared Spectra

(2012) Ann Marie Woys et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Identifying Residual Structure in Intrinsically Disordered Systems: A 2D IR Spectroscopic Study of the GVGXPGVG Peptide

(2012) Joshua Lessing et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

(2012) Marcus D Hanwell et al.   Journal of Cheminformatics

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

(2011) Santanu Roy et al.   JOURNAL OF CHEMICAL PHYSICS

Development and Validation of Transferable Amide I Vibrational Frequency Maps for Peptides

(2011) L. Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

2DIR Spectroscopy of Human Amylin Fibrils Reflects Stable β-Sheet Structure

(2011) Lu Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Residue-Specific Vibrational Echoes Yield 3D Structures of a Transmembrane Helix Dimer

(2011) A. Remorino et al.   SCIENCE

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models

(2010) Pär Bjelkmar et al.   Journal of Chemical Theory and Computation

Quantitative Assessment of Force Fields on Both Low-Energy Conformational Basins and Transition-State Regions of the (ϕ−ψ) Space

(2010) Zhiwei Liu et al.   Journal of Chemical Theory and Computation

Comparative Study of Electrostatic Models for the Amide-I and -II Modes: Linear and Two-Dimensional Infrared Spectra

(2010) Hiroaki Maekawa et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Melting of a β-Hairpin Peptide Using Isotope-Edited 2D IR Spectroscopy and Simulations

(2010) Adam W. Smith et al.   JOURNAL OF PHYSICAL CHEMISTRY B

2D IR Line Shapes Probe Ovispirin Peptide Conformation and Depth in Lipid Bilayers

(2010) Ann Marie Woys et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Vibrational solvatochromism and electrochromism: Coarse-grained models and their relationships

(2009) Minhaeng Cho   JOURNAL OF CHEMICAL PHYSICS

Toward Detecting the Formation of a Single Helical Turn by 2D IR Cross Peaks between the Amide-I and -II Modes

(2009) Hiroaki Maekawa et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides

(2009) Kaicong Cai et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Two-dimensional IR spectroscopy and isotope labeling defines the pathway of amyloid formation with residue-specific resolution

(2009) S.-H. Shim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amide I Two-Dimensional Infrared Spectroscopy of Proteins

(2008) Ziad Ganim et al.   ACCOUNTS OF CHEMICAL RESEARCH

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation