scholarly article | Q13442814 |
P50 | author | Robert B. Best | Q41049035 |
Benjamin Schuler | Q42316868 | ||
P2093 | author name string | Daniel Nettels | |
Hagen Hofmann | |||
P2860 | cites work | Energy transfer: a spectroscopic ruler | Q24618609 |
Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations | Q26822885 | ||
Structural heterogeneity and quantitative FRET efficiency distributions of polyprolines through a hybrid atomistic simulation and Monte Carlo approach | Q27342193 | ||
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation | Q27860944 | ||
Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins | Q37469603 | ||
Temperature-dependent solvation modulates the dimensions of disordered proteins | Q37702019 | ||
Multicolor single-molecule FRET to explore protein folding and binding | Q37770057 | ||
Protein folding under mechanical forces: a physiological view | Q38070971 | ||
Optimizing Protein-Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field | Q39275621 | ||
Effect of librational motion on fluorescence depolarization and nuclear magnetic resonance relaxation in macromolecules and membranes | Q41112865 | ||
Atomistic folding simulations of the five-helix bundle protein λ(6−85). | Q42012438 | ||
Urea-induced unfolding of the immunity protein Im9 monitored by spFRET. | Q42720457 | ||
Using molecular dynamics and quantum mechanics calculations to model fluorescence observables | Q42726873 | ||
Simulation of fluorescence anisotropy experiments: probing protein dynamics | Q43203268 | ||
Optimizing solute-water van der Waals interactions to reproduce solvation free energies. | Q46006756 | ||
A nano-positioning system for macromolecular structural analysis | Q46970764 | ||
Quantitative single-molecule conformational distributions: a case study with poly-(L-proline). | Q51943872 | ||
Orientational averaging of dye molecules attached to proteins in Förster resonance energy transfer measurements: insights from a simulation study. | Q52849057 | ||
Intramolecular Distances and Dynamics from the Combined Photon Statistics of Single-Molecule FRET and Photoinduced Electron Transfer | Q59332454 | ||
Probing Protein-Chaperone Interactions with Single-Molecule Fluorescence Spectroscopy | Q59332539 | ||
Unfolded Protein and Peptide Dynamics Investigated with Single-Molecule FRET and Correlation Spectroscopy from Picoseconds to Seconds† | Q59332561 | ||
Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse | Q60490648 | ||
Accurate distance determination of nucleic acids via Förster resonance energy transfer: implications of dye linker length and rigidity | Q83363957 | ||
Theoretical studies of short polyproline systems: recalibration of a molecular ruler | Q83435385 | ||
Simulation of fluorescence resonance energy transfer experiments: effect of the dyes on protein folding | Q83585357 | ||
AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations | Q86732866 | ||
Indocyanine dyes approach free rotation at the 3' terminus of A-RNA: a comparison with the 5' terminus and consequences for fluorescence resonance energy transfer | Q87000582 | ||
Concerted dihedral rotations give rise to internal friction in unfolded proteins | Q87912069 | ||
Comparison of multiple Amber force fields and development of improved protein backbone parameters | Q27861040 | ||
A general purpose model for the condensed phases of water: TIP4P/2005 | Q29393760 | ||
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations | Q29547632 | ||
Canonical sampling through velocity rescaling | Q29616131 | ||
Single-molecule spectroscopy of protein folding dynamics--expanding scope and timescales. | Q30425834 | ||
Mapping protein collapse with single-molecule fluorescence and kinetic synchrotron radiation circular dichroism spectroscopy | Q30478703 | ||
High-resolution, single-molecule measurements of biomolecular motion | Q30501806 | ||
Are current atomistic force fields accurate enough to study proteins in crowded environments? | Q30826261 | ||
Effect of flexibility and cis residues in single-molecule FRET studies of polyproline | Q31137335 | ||
A close look at fluorescence quenching of organic dyes by tryptophan. | Q33225156 | ||
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides | Q33465189 | ||
Single-molecule fluorescence probes dynamics of barrier crossing | Q33565764 | ||
Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence. | Q33863222 | ||
Alexa dyes, a series of new fluorescent dyes that yield exceptionally bright, photostable conjugates | Q33871213 | ||
From the Cover: Charge interactions can dominate the dimensions of intrinsically disordered proteins. | Q34093140 | ||
Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy | Q34154877 | ||
How fast-folding proteins fold | Q34228223 | ||
Modest influence of FRET chromophores on the properties of unfolded proteins | Q34310142 | ||
Two-state folding observed in individual protein molecules | Q34366478 | ||
Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association | Q34503099 | ||
Benchmarking all-atom simulations using hydrogen exchange | Q34526575 | ||
Speeding up parallel GROMACS on high-latency networks | Q34615212 | ||
Single-molecule fluorescence resonance energy transfer reveals a dynamic equilibrium between closed and open conformations of syntaxin 1. | Q34788804 | ||
Coil-globule transition in the denatured state of a small protein | Q34984407 | ||
Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements | Q35315878 | ||
Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations | Q35616340 | ||
Ultrafast dynamics of protein collapse from single-molecule photon statistics. | Q35669661 | ||
Single-molecule fluorescence spectroscopy of protein folding. | Q36180888 | ||
Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation. | Q36397739 | ||
Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy. | Q36398007 | ||
Atomic-level description of ubiquitin folding | Q36762717 | ||
Simulation of structure, orientation, and energy transfer between AlexaFluor molecules attached to MscL | Q36856468 | ||
Advances in single-molecule fluorescence methods for molecular biology | Q37138480 | ||
Interplay of alpha-synuclein binding and conformational switching probed by single-molecule fluorescence. | Q37153744 | ||
P433 | issue | 11 | |
P407 | language of work or name | English | Q1860 |
P921 | main subject | force field | Q1341441 |
P304 | page(s) | 2721-2731 | |
P577 | publication date | 2015-06-01 | |
P1433 | published in | Biophysical Journal | Q2032955 |
P1476 | title | Quantitative interpretation of FRET experiments via molecular simulation: force field and validation | |
P478 | volume | 108 |
Q46470776 | An atomistic view on carbocyanine photophysics in the realm of RNA. |
Q46062001 | An in vitro tag-and-modify protein sample generation method for single-molecule fluorescence resonance energy transfer |
Q41411613 | Combining Graphical and Analytical Methods with Molecular Simulations To Analyze Time-Resolved FRET Measurements of Labeled Macromolecules Accurately |
Q55513394 | Dynamic action of the Sec machinery during initiation, protein translocation and termination. |
Q40315584 | Empirical Optimization of Interactions between Proteins and Chemical Denaturants in Molecular Simulations |
Q59332391 | Excited-state annihilation reduces power dependence of single-molecule FRET experiments |
Q47591502 | Force field development and simulations of intrinsically disordered proteins |
Q59332309 | Inferring properties of disordered chains from FRET transfer efficiencies |
Q90561582 | Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations |
Q55040516 | Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning. |
Q60194855 | Lipid Configurations from Molecular Dynamics Simulations |
Q41110746 | Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment. |
Q52616567 | Simulation of FRET dyes allows quantitative comparison against experimental data. |
Q47348403 | Theory of FRET "Spectroscopic Ruler" for Short Distances: Application to Polyproline |
Search more.