(Q35021407)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16844758%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

title

Spectral signatures of heterogeneous protein ensembles revealed by MD Simulations of 2DIR spectra (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16844758%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16844758%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

2

Andrei Tokmakoff

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16844758%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

language of work or name

English

0 references

publication date

14 July 2006

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16844758%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

number of pages

11

1 reference

inferred from page(s)

published in

Biophysical Journal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16844758%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

volume

91

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16844758%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

issue

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16844758%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

page(s)

2636-2646

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16844758%20AND%20SRC:MED&resulttype=core&format=json

All-atom empirical potential for molecular modeling and dynamics studies of proteins

27 December 2019

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Amide I vibrational dynamics of N-methylacetamide in polar solvents: the role of electrostatic interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Simulation protocols for coherent femtosecond vibrational spectra of peptides

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

A transferable electrostatic map for solvation effects on amide I vibrations and its application to linear and two-dimensional spectroscopy

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Evaluation of the information content in infrared spectra for protein secondary structure determination

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Folding mechanism of beta-hairpins studied by replica exchange molecular simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Ab initio-based exciton model of amide I vibrations in peptides: definition, conformational dependence, and transferability.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Kinetic pathways of beta-hairpin (un)folding in explicit solvent

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Empirical force fields for biological macromolecules: overview and issues.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Simulations of the role of water in the protein-folding mechanism

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Core structure of amyloid fibril proposed from IR-microscope linear dichroism

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Drying-induced hydrophobic polymer collapse

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Temperature-dependent helix-coil transition of an alanine based peptide

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Tryptophan zippers: Stable, monomeric -hairpins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

The key event in force-induced unfolding of Titin's immunoglobulin domains

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Understanding beta-hairpin formation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Folding dynamics and mechanism of beta-hairpin formation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Intermolecular Interaction Effects in the Amide I Vibrations of β Polypeptides

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Unusually stable helix formation in short alanine-based peptides

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Simulation studies of amide I IR absorption and two-dimensional IR spectra of beta hairpins in liquid water.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Collective oscillations and the linear and two-dimensional infrared spectra of inhomogeneous beta-sheets.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Electrostatic DFT map for the complete vibrational amide band of NMA.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Vibrational spectral simulation for peptides of mixed secondary structure: method comparisons with the Trpzip model hairpin.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Stochastic Liouville equation simulation of multidimensional vibrational line shapes of trialanine

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: Comparison of different electronic structure/molecular dynamics approaches

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Structure of bovine pancreatic trypsin inhibitor at 125 K definition of carboxyl-terminal residues Gly57 and Ala58.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

The structure of tri-proline in water probed by polarized Raman, Fourier transform infrared, vibrational circular dichroism, and electric ultraviolet circular dichroism spectroscopy

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Vibrational Stark effects calibrate the sensitivity of vibrational probes for electric fields in proteins

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Vibrational spectroscopy and the development of new force fields for biological molecules

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Molecular dynamics simulations of hydrophobic collapse of ubiquitin

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Residual Native Structure in a Thermally Denatured β-Hairpin

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1562382

Evidence of turn and salt bridge contributions to beta-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G

9 December 2018

1 reference

12 December 2020

Signatures of beta-sheet secondary structures in linear and two-dimensional infrared spectroscopy

1 reference

12 December 2020

The mechanism of beta-hairpin formation

1 reference

12 December 2020

Structure of Synthetic Polypeptides

1 reference

12 December 2020

Application of the local regression method interval partial least-squares to the elucidation of protein secondary structure

1 reference

12 December 2020

Visualization and characterization of the infrared active amide I vibrations of proteins

1 reference

12 December 2020

Electric field fluctuations drive vibrational dephasing in water

1 reference

12 December 2020

Understanding normal modes of proteins

1 reference

12 December 2020

10.1529/BIOPHYSJ.106.088070

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16844758%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16844758%20AND%20SRC:MED&resulttype=core&format=json

27 December 2019

PubMed publication ID

16844758

1 reference