Published in PLoS Comput Biol on March 21, 2008
Structural characterization of IrisFP, an optical highlighter undergoing multiple photo-induced transformations. Proc Natl Acad Sci U S A (2008) 1.68
Chromophore transformations in red fluorescent proteins. Chem Rev (2012) 1.08
Modern fluorescent proteins: from chromophore formation to novel intracellular applications. Biotechniques (2011) 0.96
Stochastic approach to the molecular counting problem in superresolution microscopy. Proc Natl Acad Sci U S A (2014) 0.92
Beta-barrel scaffold of fluorescent proteins: folding, stability and role in chromophore formation. Int Rev Cell Mol Biol (2013) 0.89
A structural basis for reversible photoswitching of absorbance spectra in red fluorescent protein rsTagRFP. J Mol Biol (2012) 0.88
Computer modeling of the structure and spectra of fluorescent proteins. Acta Naturae (2009) 0.84
Phototransformable fluorescent proteins: which one for which application? Histochem Cell Biol (2014) 0.84
Excited-State Electronic Structure with Configuration Interaction Singles and Tamm-Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units. J Chem Theory Comput (2011) 0.83
Molecular mechanism of a green-shifted, pH-dependent red fluorescent protein mKate variant. PLoS One (2011) 0.82
Ground-state proton transfer in the photoswitching reactions of the fluorescent protein Dronpa. Nat Commun (2013) 0.79
Conformation dependence of pKa's of the chromophores from the purple asFP595 and yellow zFP538 fluorescent proteins. Theochem (2008) 0.76
Mechanism and bottlenecks in strand photodissociation of split green fluorescent proteins (GFPs). Proc Natl Acad Sci U S A (2017) 0.75
The green fluorescent protein. Annu Rev Biochem (1998) 34.17
GROMACS: fast, flexible, and free. J Comput Chem (2005) 27.22
WHAT IF: a molecular modeling and drug design program. J Mol Graph (1990) 24.35
Essential dynamics of proteins. Proteins (1993) 11.56
Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol (1976) 9.91
Toward fluorescence nanoscopy. Nat Biotechnol (2003) 8.63
Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins. Proc Natl Acad Sci U S A (2005) 6.65
Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting. Science (2004) 6.52
An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein. Proc Natl Acad Sci U S A (2002) 6.37
Natural animal coloration can Be determined by a nonfluorescent green fluorescent protein homolog. J Biol Chem (2000) 6.12
Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-A resolution. Proc Natl Acad Sci U S A (2001) 6.06
Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins (1996) 5.83
Large-amplitude nonlinear motions in proteins. Phys Rev Lett (1992) 5.15
Innovation: Photoactivatable fluorescent proteins. Nat Rev Mol Cell Biol (2005) 4.37
Reversible single-molecule photoswitching in the GFP-like fluorescent protein Dronpa. Proc Natl Acad Sci U S A (2005) 4.01
Semi-rational engineering of a coral fluorescent protein into an efficient highlighter. EMBO Rep (2005) 3.45
Bicycle-pedal model for the first step in the vision process. Nature (1976) 3.13
Photobleaching and photoactivation: following protein dynamics in living cells. Nat Cell Biol (2003) 3.09
Kindling fluorescent proteins for precise in vivo photolabeling. Nat Biotechnol (2003) 3.08
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc (1988) 3.07
Predicting slow structural transitions in macromolecular systems: Conformational flooding. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics (1995) 2.88
Fluorescent proteins: maturation, photochemistry and photophysics. Curr Opin Struct Biol (2006) 2.53
1.8 A bright-state structure of the reversibly switchable fluorescent protein Dronpa guides the generation of fast switching variants. Biochem J (2007) 2.33
The 2.0-A crystal structure of eqFP611, a far red fluorescent protein from the sea anemone Entacmaea quadricolor. J Biol Chem (2003) 2.23
Structure and mechanism of the reversible photoswitch of a fluorescent protein. Proc Natl Acad Sci U S A (2005) 2.21
Chromophore environment provides clue to "kindling fluorescent protein" riddle. J Biol Chem (2002) 2.19
A far-red fluorescent protein with fast maturation and reduced oligomerization tendency from Entacmaea quadricolor (Anthozoa, Actinaria). Proc Natl Acad Sci U S A (2002) 2.15
Structural basis for reversible photoswitching in Dronpa. Proc Natl Acad Sci U S A (2007) 2.08
Kindling fluorescent protein from Anemonia sulcata: dark-state structure at 1.38 A resolution. Biochemistry (2005) 1.96
Phototransformation of green fluorescent protein with UV and visible light leads to decarboxylation of glutamate 222. Nat Struct Biol (2002) 1.94
Lighting up cells: labelling proteins with fluorophores. Nat Cell Biol (2003) 1.87
Concepts for nanoscale resolution in fluorescence microscopy. Curr Opin Neurobiol (2004) 1.75
Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein. J Am Chem Soc (2004) 1.65
The 2.2 A crystal structure of a pocilloporin pigment reveals a nonplanar chromophore conformation. Structure (2003) 1.61
Evidence for the isomerization and decarboxylation in the photoconversion of the red fluorescent protein DsRed. J Am Chem Soc (2005) 1.44
Isomerization through conical intersections. Annu Rev Phys Chem (2007) 1.43
Reversible molecular photoswitches: a key technology for nanoscience and fluorescence imaging. Proc Natl Acad Sci U S A (2005) 1.42
Observation of excited-state proton transfer in green fluorescent protein using ultrafast vibrational spectroscopy. J Am Chem Soc (2005) 1.41
Proton pathways in green fluorescence protein. Biophys J (2005) 1.36
Synthesis and properties of the chromophore of the asFP595 chromoprotein from Anemonia sulcata. Biochemistry (2005) 1.36
Light-driven decarboxylation of wild-type green fluorescent protein. J Am Chem Soc (2003) 1.34
Highlighted generation of fluorescence signals using simultaneous two-color irradiation on Dronpa mutants. Biophys J (2007) 1.32
The 1.7 A crystal structure of Dronpa: a photoswitchable green fluorescent protein. J Mol Biol (2006) 1.29
The 2.1A crystal structure of the far-red fluorescent protein HcRed: inherent conformational flexibility of the chromophore. J Mol Biol (2005) 1.23
Variations on the GFP chromophore: A polypeptide fragmentation within the chromophore revealed in the 2.1-A crystal structure of a nonfluorescent chromoprotein from Anemonia sulcata. J Biol Chem (2004) 1.21
Photo-induced protonation/deprotonation in the GFP-like fluorescent protein Dronpa: mechanism responsible for the reversible photoswitching. Photochem Photobiol Sci (2006) 1.18
Properties of the emitting state of the green fluorescent protein resolved at the CASPT2//CASSCF/CHARMM level. J Am Chem Soc (2005) 1.07
Photoswitching of the fluorescent protein asFP595: mechanism, proton pathways, and absorption spectra. Angew Chem Int Ed Engl (2007) 1.06
Fast and reversible photoswitching of the fluorescent protein dronpa as evidenced by fluorescence correlation spectroscopy. Biophys J (2006) 1.04
Transition in the temperature-dependence of GFP fluorescence: from proton wires to proton exit. Biophys J (2005) 1.03
Ultrafast deactivation of an excited cytosine-guanine base pair in DNA. J Am Chem Soc (2007) 1.02
Conical intersection dynamics in solution: the chromophore of Green Fluorescent Protein. Faraday Discuss (2004) 1.01
Origin, nature, and fate of the fluorescent state of the green fluorescent protein chromophore at the CASPT2//CASSCF resolution. J Am Chem Soc (2004) 1.01
Radiationless decay of red fluorescent protein chromophore models via twisted intramolecular charge-transfer states. J Am Chem Soc (2007) 1.00
Ultrafast excited-state dynamics of the photoswitchable protein Dronpa. J Am Chem Soc (2007) 0.99
Flooding in GROMACS: accelerated barrier crossings in molecular dynamics. J Comput Chem (2006) 0.97
Photoconversion in the red fluorescent protein from the sea anemone Entacmaea quadricolor: is cis-trans isomerization involved? J Am Chem Soc (2006) 0.95
Crystallization and preliminary X-ray diffraction analysis of the red fluorescent protein eqFP611. Acta Crystallogr D Biol Crystallogr (2003) 0.94
Insights for light-driven molecular devices from ab initio multiple spawning excited-state dynamics of organic and biological chromophores. Acc Chem Res (2006) 0.89
Solvent effects on the vibrational activity and photodynamics of the green fluorescent protein chromophore: a quantum-chemical study. J Am Chem Soc (2005) 0.88
Potential energy landscape of the photoinduced multiple proton-transfer process in the green fluorescent protein: classical molecular dynamics and multiconfigurational electronic structure calculations. J Am Chem Soc (2006) 0.86
Electronic excitations of biomolecules studied by quantum chemistry. Curr Opin Struct Biol (2002) 0.85
Electronic Excitations of the Chromophore from the Fluorescent Protein asFP595 in Solutions. J Chem Theory Comput (2006) 0.79
Ground-state structures and vertical excitations for the kindling fluorescent protein asFP595. J Phys Chem B (2006) 0.77
The chromophore of asFP595: a theoretical study. J Phys Chem B (2006) 0.77
Photostability via a sloped conical intersection: a CASSCF and RASSCF study of pyracylene. J Phys Chem A (2005) 0.76
GROMACS: fast, flexible, and free. J Comput Chem (2005) 27.22
Molecular anatomy of a trafficking organelle. Cell (2006) 11.47
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science (2008) 8.04
Anatomy and dynamics of a supramolecular membrane protein cluster. Science (2007) 3.75
Membrane protein sequestering by ionic protein-lipid interactions. Nature (2011) 2.40
Effect of sodium chloride on a lipid bilayer. Biophys J (2003) 2.24
Structure and mechanism of the reversible photoswitch of a fluorescent protein. Proc Natl Acad Sci U S A (2005) 2.21
Sequential N- to C-terminal SNARE complex assembly drives priming and fusion of secretory vesicles. EMBO J (2006) 2.19
Mechanoenzymatics of titin kinase. Proc Natl Acad Sci U S A (2008) 2.17
Generalized correlation for biomolecular dynamics. Proteins (2006) 2.17
g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. J Comput Chem (2010) 2.08
Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase. Nat Struct Biol (2002) 1.92
The mechanism of proton exclusion in the aquaporin-1 water channel. J Mol Biol (2003) 1.80
Force spectroscopy of single biomolecules. Chemphyschem (2002) 1.73
Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations. Biophys J (2004) 1.70
The dynamics and energetics of water permeation and proton exclusion in aquaporins. Curr Opin Struct Biol (2005) 1.65
Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein. J Am Chem Soc (2004) 1.65
Single-molecule FRET measures bends and kinks in DNA. Proc Natl Acad Sci U S A (2008) 1.58
Structure and function of water channels. Curr Opin Struct Biol (2002) 1.55
Multistep binding of divalent cations to phospholipid bilayers: a molecular dynamics study. Angew Chem Int Ed Engl (2004) 1.50
Full correlation analysis of conformational protein dynamics. Proteins (2008) 1.47
Quaternary ammonium compounds as water channel blockers. Specificity, potency, and site of action. J Biol Chem (2006) 1.46
Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations. Biophys J (2008) 1.43
Energy barriers and driving forces in tRNA translocation through the ribosome. Nat Struct Mol Biol (2013) 1.41
Synaptotagmin-1 may be a distance regulator acting upstream of SNARE nucleation. Nat Struct Mol Biol (2011) 1.41
Interaction of urea with amino acids: implications for urea-induced protein denaturation. J Am Chem Soc (2007) 1.39
Phosphatidylinositol 4,5-bisphosphate clusters act as molecular beacons for vesicle recruitment. Nat Struct Mol Biol (2013) 1.38
Water permeation through gramicidin A: desformylation and the double helix: a molecular dynamics study. Biophys J (2002) 1.37
Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics. J Biomol NMR (2008) 1.33
Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail. Biophys J (2011) 1.30
Membrane fusion. Curr Opin Cell Biol (2002) 1.29
How SNARE molecules mediate membrane fusion: recent insights from molecular simulations. Curr Opin Struct Biol (2012) 1.26
Mechanical properties of the icosahedral shell of southern bean mosaic virus: a molecular dynamics study. Biophys J (2009) 1.26
Caught in the act: visualization of SNARE-mediated fusion events in molecular detail. Chembiochem (2011) 1.25
Speeding up parallel GROMACS on high-latency networks. J Comput Chem (2007) 1.23
Detecting protein-induced folding of the U4 snRNA kink-turn by single-molecule multiparameter FRET measurements. RNA (2005) 1.23
Simulation of fluorescence anisotropy experiments: probing protein dynamics. Biophys J (2005) 1.21
Differential peptide dynamics is linked to major histocompatibility complex polymorphism. J Biol Chem (2004) 1.19
Collective Langevin dynamics of conformational motions in proteins. J Chem Phys (2006) 1.18
Structural heterogeneity and quantitative FRET efficiency distributions of polyprolines through a hybrid atomistic simulation and Monte Carlo approach. PLoS One (2011) 1.16
Aqueous urea solutions: structure, energetics, and urea aggregation. J Phys Chem B (2007) 1.16
Light-induced structural changes in a photosynthetic reaction center caught by Laue diffraction. Science (2010) 1.15
Can principal components yield a dimension reduced description of protein dynamics on long time scales? J Phys Chem B (2006) 1.12
Synthesis, structure, and magnetic properties of an antiferromagnetic spin-ladder complex: bis(2,3-dimethylpyridinium) tetrabromocuprate. J Am Chem Soc (2007) 1.11
Quantitative structural analysis of importin-β flexibility: paradigm for solenoid protein structures. Structure (2010) 1.11
Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics. J Chem Theory Comput (2011) 1.09
Mechanical properties of single motor molecules studied by three-dimensional thermal force probing in optical tweezers. Chemphyschem (2004) 1.09
Kinetics of conformational sampling in ubiquitin. Angew Chem Int Ed Engl (2011) 1.07
Ultrafast decay of electronically excited singlet cytosine via a pi,pi* to n(O),pi* state switch. J Am Chem Soc (2002) 1.07
Photoswitching of the fluorescent protein asFP595: mechanism, proton pathways, and absorption spectra. Angew Chem Int Ed Engl (2007) 1.06
Influenza virus binds its host cell using multiple dynamic interactions. Proc Natl Acad Sci U S A (2012) 1.05
Ultrafast deactivation channel for thymine dimerization. J Am Chem Soc (2007) 1.04
Torsional elasticity and energetics of F1-ATPase. Proc Natl Acad Sci U S A (2011) 1.03
Ultrafast deactivation of an excited cytosine-guanine base pair in DNA. J Am Chem Soc (2007) 1.02
An unusual hydrophobic core confers extreme flexibility to HEAT repeat proteins. Biophys J (2010) 1.02
Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations? Handb Exp Pharmacol (2009) 1.02
Voltage-regulated water flux through aquaporin channels in silico. Biophys J (2010) 1.01
Kinase-activity-independent functions of atypical protein kinase C in Drosophila. J Cell Sci (2009) 1.00
Molecular basis of the light-driven switching of the photochromic fluorescent protein Padron. J Biol Chem (2010) 0.99
Polar or apolar--the role of polarity for urea-induced protein denaturation. PLoS Comput Biol (2008) 0.99
Structural basis for cooperativity of CRM1 export complex formation. Proc Natl Acad Sci U S A (2012) 0.98
Position of transmembrane helix 6 determines receptor G protein coupling specificity. J Am Chem Soc (2014) 0.98
Fluctuations of primary ubiquitin folding intermediates in a force clamp. J Struct Biol (2006) 0.98
Mechanical coupling via the membrane fusion SNARE protein syntaxin 1A: a molecular dynamics study. Biophys J (2003) 0.97
Flooding in GROMACS: accelerated barrier crossings in molecular dynamics. J Comput Chem (2006) 0.97
A molecular dynamics study of slow base flipping in DNA using conformational flooding. Biophys J (2007) 0.93
Urea impedes the hydrophobic collapse of partially unfolded proteins. Biophys J (2009) 0.93
Primary changes of the mechanical properties of Southern Bean Mosaic Virus upon calcium removal. Biophys J (2010) 0.93
Conformational dynamics of the F1-ATPase beta-subunit: a molecular dynamics study. Biophys J (2003) 0.93
Exploring protein dynamics space: the dynasome as the missing link between protein structure and function. PLoS One (2012) 0.93
Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions. Angew Chem Int Ed Engl (2005) 0.91
Arginine52 controls the photoisomerization process in photoactive yellow protein. J Am Chem Soc (2008) 0.91
Importin-beta: structural and dynamic determinants of a molecular spring. Structure (2008) 0.91
Residual dipolar couplings as a tool to study molecular recognition of ubiquitin. Biochem Soc Trans (2008) 0.90
Is TEA an inhibitor for human Aquaporin-1? Pflugers Arch (2008) 0.90
Rotation triggers nucleotide-independent conformational transition of the empty β subunit of F₁-ATPase. J Am Chem Soc (2014) 0.89
Quantitative assessment of protein interaction with methyl-lysine analogues by hybrid computational and experimental approaches. ACS Chem Biol (2011) 0.89
Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes. J Comput Chem (2009) 0.89
Estimation of absolute solvent and solvation shell entropies via permutation reduction. J Chem Phys (2007) 0.89
Linear-scaling soft-core scheme for alchemical free energy calculations. J Comput Chem (2011) 0.89
A highly strained nuclear conformation of the exportin Cse1p revealed by molecular dynamics simulations. Structure (2006) 0.89
The structure of the aquaporin-1 water channel: a comparison between cryo-electron microscopy and X-ray crystallography. J Mol Biol (2003) 0.88
Intramolecular charge transfer in 4-aminobenzonitriles does not necessarily need the twist. J Am Chem Soc (2005) 0.88
Elastic properties of photoswitchable azobenzene polymers from molecular dynamics simulations. Angew Chem Int Ed Engl (2007) 0.87
A "force buffer" protecting immunoglobulin titin. Angew Chem Int Ed Engl (2010) 0.87
Line-tension controlled mechanism for influenza fusion. PLoS One (2012) 0.87
Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in high-dimensional configuration spaces. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.85