Related references
Note: Only part of the references are listed.Distinguishing islet amyloid polypeptide fibril structures with infrared isotope-label spectroscopy
Vishesh Saxena et al.
JOURNAL OF CHEMICAL PHYSICS (2022)
Distinct electrostatic frequency tuning rates for amide I and amide I′ vibrations
Kevin Chelius et al.
JOURNAL OF CHEMICAL PHYSICS (2021)
Computational spectroscopy of complex systems
Thomas L. C. Jansen
JOURNAL OF CHEMICAL PHYSICS (2021)
iSPECTRON: A simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software
Francesco Segatta et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2021)
Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c
Youssef El Khoury et al.
JOURNAL OF CHEMICAL PHYSICS (2021)
Highly accurate protein structure prediction with AlphaFold
John Jumper et al.
NATURE (2021)
IR Spectroscopy Can Reveal the Mechanism of K+ Transport in Ion Channels
Steven E. Strong et al.
BIOPHYSICAL JOURNAL (2020)
Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction
Carlos R. Baiz et al.
CHEMICAL REVIEWS (2020)
Scalable molecular dynamics on CPU and GPU architectures with NAMD
James C. Phillips et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Array programming with NumPy
Charles R. Harris et al.
NATURE (2020)
Dynamics and Infrared Spectrocopy of Monomeric and Dimeric Wild Type and Mutant Insulin
Seyedeh Maryam Salehi et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2020)
Theory of coherent two-dimensional vibrational spectroscopy
Thomas la Cour Jansen et al.
JOURNAL OF CHEMICAL PHYSICS (2019)
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
Stephen K. Burley et al.
NUCLEIC ACIDS RESEARCH (2019)
Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels
Wojciech Kopec et al.
NATURE CHEMISTRY (2018)
NGLview-interactive molecular graphics for Jupyter notebooks
Hai Nguyen et al.
BIOINFORMATICS (2018)
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Jing Huang et al.
NATURE METHODS (2017)
Interplay between Hydrogen Bonding and Vibrational Coupling in Liquid N-Methylacetamide
Ana V. Cunha et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2017)
Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED
M. Jason de la Cruz et al.
NATURE METHODS (2017)
Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics
Mike Reppert et al.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 67 (2016)
Assessing Spectral Simulation Protocols for the Amide I Band of Proteins
Ana V. Cunha et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Application of two-dimensional infrared spectroscopy to benchmark models for the amide I band of proteins
Anna S. Bondarenko et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling
Paul Stevenson et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
Electrostatic frequency shifts in amide I vibrational spectra: Direct parameterization against experiment
Mike Reppert et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Folding Dynamics of the Trp-Cage Miniprotein: Evidence for a Native-Like Intermediate from Combined Time-Resolved Vibrational Spectroscopy and Molecular Dynamics Simulations
Heleen Meuzelaar et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
An overview of the Amber biomolecular simulation package
Romelia Salomon-Ferrer et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2013)
Coherent two-dimensional infrared spectroscopy: Quantitative analysis of protein secondary structure in solution
Carlos R. Baiz et al.
ANALYST (2012)
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
Ann Marie Woys et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)
Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline
Santanu Roy et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Software News and Updates MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations
Naveen Michaud-Agrawal et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
Modeling the Vibrational Dynamics and Nonlinear Infrared Spectra of Coupled Amide I and II Modes in Peptides
Arend G. Dijkstra et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2011)
Development and Validation of Transferable Amide I Vibrational Frequency Maps for Peptides
L. Wang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2011)
2DIR Spectroscopy of Human Amylin Fibrils Reflects Stable β-Sheet Structure
Lu Wang et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)
Software News and Update Reconstruction of Atomistic Details from Coarse-Grained Structures
Andrzej J. Rzepiela et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2010)
Melting of a β-Hairpin Peptide Using Isotope-Edited 2D IR Spectroscopy and Simulations
Adam W. Smith et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Structural classification of the amide I sites of a beta-hairpin with isotope label 2DIR spectroscopy
Santanu Roy et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2010)
Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy
Ziad Ganim et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2010)
Amide I′-II′ 2D IR Spectroscopy Provides Enhanced Protein Secondary Structural Sensitivity
Lauren P. DeFlores et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Gating Mechanism of the Influenza A M2 Channel Revealed by 1D and 2D IR Spectroscopies
Joshua Manor et al.
STRUCTURE (2009)
Vibrational-exciton couplings for the amide i, II, III, and a modes of peptides
Tomoyuki Hayashi et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Transient 2D IR spectroscopy of ubiquitin unfolding dynamics
Hoi Sung Chung et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Canonical sampling through velocity rescaling
Giovanni Bussi et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Infrared spectroscopy of proteins
Andreas Barth
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2007)
Water penetration into protein secondary structure revealed by hydrogen-deuterium exchange two-dimensional infrared spectroscopy
Lauren P. DeFlores et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Nonadiabatic effects in the two-dimensional infrared spectra of peptides: Application to alanine dipeptide
Thomas la Cour Jansen et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Spectral signatures of heterogeneous protein ensembles revealed by MD simulations of 2DIR spectra
Ziad Ganim et al.
BIOPHYSICAL JOURNAL (2006)
Modeling the amide I bands of small peptides
Thomas la Cour Jansen et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Stretched versus compressed exponential kinetics in α-helix folding
P Hamm et al.
CHEMICAL PHYSICS (2006)
Different spectral signatures of octapeptide 310 and α-helices revealed by two-dimensional infrared spectroscopy
H Maekawa et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
A transferable electrostatic map for solvation effects on amide I vibrations and its application to linear and two-dimensional spectroscopy
TL Jansen et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
GROMACS: Fast, flexible, and free
D Van der Spoel et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Vibrational relaxation of the bending mode of HDO in liquid D2O
P Bodis et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2005)
Theoretical studies of the amide I vibrational frequencies of [Leu]-enkephalin
TM Watson et al.
MOLECULAR PHYSICS (2005)
Amide I vibrational dynamics of N-methylacetamide in polar solvents:: The role of electrostatic interactions
MF DeCamp et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Molecular dynamics and protein function
M Karplus et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Signatures of β-sheet secondary structures in linear and two-dimensional infrared spectroscopy
CM Cheatum et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Amide I vibrational circular dichroism of dipeptide: Conformation dependence and fragment analysis
JH Choi et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Amide I modes in the N-methylacetamide dimer and glycine dipeptide analog:: Diagonal force constants
S Ham et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Intrinsic disorder and protein function
AK Dunker et al.
BIOCHEMISTRY (2002)
Coupling of the amide I modes of the glycine dipeptide
P Hamm et al.
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN (2002)
Time-resolved two-dimensional vibrational spectroscopy of a short α-helix in water
S Woutersen et al.
JOURNAL OF CHEMICAL PHYSICS (2001)