Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies

Complex RNA Folding Kinetics Revealed by Single-Molecule FRET and Hidden Markov Models

(2014) Bettina G. Keller et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Combining Experiments and Simulations Using the Maximum Entropy Principle

(2014) Wouter Boomsma et al.   PLoS Computational Biology

Photophysical processes in single molecule organic fluorescent probes

(2013) Elana M. S. Stennett et al.   CHEMICAL SOCIETY REVIEWS

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

(2013) Benoît Roux et al.   JOURNAL OF CHEMICAL PHYSICS

Single-Molecule FRET Reveals the Native-State Dynamics of the IκBα Ankyrin Repeat Domain

(2013) Jorge A. Lamboy et al.   JOURNAL OF MOLECULAR BIOLOGY

Detection of Dihydrofolate Reductase Conformational Change by FRET Using Two Fluorescent Amino Acids

(2013) Shengxi Chen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Labeling Proteins with Fluorophore/Thioamide Förster Resonant Energy Transfer Pairs by Combining Unnatural Amino Acid Mutagenesis and Native Chemical Ligation

(2013) Rebecca F. Wissner et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Transport dynamics in a glutamate transporter homologue

(2013) Nurunisa Akyuz et al.   NATURE

Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics

(2013) Shuangluo Xia et al.   NUCLEIC ACIDS RESEARCH

FRET between a donor and an acceptor covalently bound to human serum albumin in native and non-native states

(2013) Rajdeep Chowdhury et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Maximum likelihood-based analysis of photon arrival trajectories in single-molecule FRET

(2012) Marta Waligórska et al.   CHEMICAL PHYSICS

In silico FRET from simulated dye dynamics

(2012) Martin Hoefling et al.   COMPUTER PHYSICS COMMUNICATIONS

On the Use of Experimental Observations to Bias Simulated Ensembles

(2012) Jed W. Pitera et al.   Journal of Chemical Theory and Computation

New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field

(2012) Maria M. Reif et al.   Journal of Chemical Theory and Computation

Native State Conformational Heterogeneity of HP35 Revealed by Time-Resolved FRET

(2012) Arnaldo L. Serrano et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Theory of the energy transfer efficiency and fluorescence lifetime distribution in single-molecule FRET

(2012) I. V. Gopich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FRET detection of amyloid β-peptide oligomerization using a fluorescent protein probe presenting a pseudo-amyloid structure

(2011) Tsuyoshi Takahashi et al.   CHEMICAL COMMUNICATIONS

Single-Molecule FRET Ruler Based on Rigid DNA Origami Blocks

(2011) Ingo H. Stein et al.   CHEMPHYSCHEM

Fluorescence Anisotropy of Molecular Rotors

(2011) James A. Levitt et al.   CHEMPHYSCHEM

Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation

(2011) Nathan Schmid et al.   COMPUTER PHYSICS COMMUNICATIONS

GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories

(2011) Andreas P. Eichenberger et al.   Journal of Chemical Theory and Computation

Time-Resolved FRET Detection of Subtle Temperature-Induced Conformational Biases in Ensembles of α-Synuclein Molecules

(2011) Asaf Grupi et al.   JOURNAL OF MOLECULAR BIOLOGY

Sensitivity of Amyloid Formation by Human Islet Amyloid Polypeptide to Mutations at Residue 20

(2011) Ping Cao et al.   JOURNAL OF MOLECULAR BIOLOGY

Förster resonance energy transfer – A spectroscopic nanoruler: Principle and applications

(2011) Harekrushna Sahoo   JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS

Effect of Aggregation on the Photophysical Properties of Three Fluorene–Phenylene-Based Cationic Conjugated Polyelectrolytes

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

Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein

(2011) Menahem Pirchi et al.   Nature Communications

Modulation ofp-Cyanophenylalanine Fluorescence by Amino Acid Side Chains and Rational Design of Fluorescence Probes of α-Helix Formation

(2010) Humeyra Taskent-Sezgin et al.   BIOCHEMISTRY

Photophysics of a fluorescent non-natural amino acid: p -Cyanophenylalanine

(2010) Arnaldo L. Serrano et al.   CHEMICAL PHYSICS LETTERS

Probing Protein Folding Using Site-Specifically Encoded Unnatural Amino Acids as FRET Donors with Tryptophan

(2009) Shigeki J. Miyake-Stoner et al.   BIOCHEMISTRY

Protein dynamics from single-molecule fluorescence intensity correlation functions

(2009) Irina V. Gopich et al.   JOURNAL OF CHEMICAL PHYSICS

Decoding the Pattern of Photon Colors in Single-Molecule FRET

(2009) Irina V. Gopich et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Using an Amino Acid Fluorescence Resonance Energy Transfer Pair To Probe Protein Unfolding: Application to the Villin Headpiece Subdomain and the LysM Domain†

(2008) Julie M. Glasscock et al.   BIOCHEMISTRY

The Fluorescent Amino Acidp-Cyanophenylalanine Provides an Intrinsic Probe of Amyloid Formation

(2008) Peter Marek et al.   CHEMBIOCHEM

Molecular simulation as an aid to experimentalists

(2008) Wilfred F van Gunsteren et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A practical guide to single-molecule FRET

(2008) Rahul Roy et al.   NATURE METHODS