Published in J Am Chem Soc on April 07, 2004
Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein. Science (2014) 2.88
Conical intersection dynamics of the primary photoisomerization event in vision. Nature (2010) 1.78
Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography. Nat Chem (2013) 1.48
Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble. PLoS Comput Biol (2014) 1.41
Ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein. Proc Natl Acad Sci U S A (2006) 1.25
Incoherent manipulation of the photoactive yellow protein photocycle with dispersed pump-dump-probe spectroscopy. Biophys J (2004) 1.24
Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein. Science (2016) 1.23
N-Ras forms dimers at POPC membranes. Biophys J (2012) 1.13
Structural evolution of the chromophore in the primary stages of trans/cis isomerization in photoactive yellow protein. J Am Chem Soc (2005) 1.04
pH dependence of the photoactive yellow protein photocycle investigated by time-resolved crystallography. Biophys J (2012) 1.03
Protein energy landscapes determined by five-dimensional crystallography. Acta Crystallogr D Biol Crystallogr (2013) 1.03
Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein. Proc Natl Acad Sci U S A (2010) 1.02
Ras and GTPase-activating protein (GAP) drive GTP into a precatalytic state as revealed by combining FTIR and biomolecular simulations. Proc Natl Acad Sci U S A (2012) 0.99
Chromophore protonation state controls photoswitching of the fluoroprotein asFP595. PLoS Comput Biol (2008) 0.96
Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein. Nat Chem (2014) 0.93
Contrasting the excited-state dynamics of the photoactive yellow protein chromophore: protein versus solvent environments. Biophys J (2004) 0.91
Predicting the signaling state of photoactive yellow protein. Biophys J (2005) 0.90
Primary steps of the photoactive yellow protein: isolated chromophore dynamics and protein directed function. Proc Natl Acad Sci U S A (2006) 0.87
Photoinduced conformational dynamics of a photoswitchable peptide: a nonequilibrium molecular dynamics simulation study. Biophys J (2006) 0.87
The role of magnesium for geometry and charge in GTP hydrolysis, revealed by quantum mechanics/molecular mechanics simulations. Biophys J (2012) 0.87
Quantum mechanical/molecular mechanical studies on spectral tuning mechanisms of visual pigments and other photoactive proteins. Photochem Photobiol (2008) 0.86
Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. J Chem Theory Comput (2012) 0.83
Hydrogen bonding controls excited-state decay of the photoactive yellow protein chromophore. J Am Chem Soc (2009) 0.83
Catching a protein in the act. Proc Natl Acad Sci U S A (2010) 0.80
Bond torsion affects the product distribution in the photoreaction of retinal model chromophores. J Mol Model (2005) 0.79
Efficient and Flexible Computation of Many-Electron Wave Function Overlaps. J Chem Theory Comput (2016) 0.78
Catalysis of GTP Hydrolysis by Small GTPases at Atomic Detail by Integration of X-ray Crystallography, Experimental, and Theoretical IR Spectroscopy. J Biol Chem (2015) 0.77
A short history of structure based research on the photocycle of photoactive yellow protein. Struct Dyn (2017) 0.75
Controlling the photoreactivity of the photoactive yellow protein chromophore by substituting at the p-coumaric acid group. J Phys Chem B (2011) 0.75
Mechanism and bottlenecks in strand photodissociation of split green fluorescent proteins (GFPs). Proc Natl Acad Sci U S A (2017) 0.75
Nonadiabatic photodynamics of a retinal model in polar and nonpolar environment. J Phys Chem A (2013) 0.75
GROMACS: fast, flexible, and free. J Comput Chem (2005) 27.22
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (2013) 11.01
A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem (2004) 8.13
Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur Biophys J (2011) 2.43
Antimicrobial peptides in action. J Am Chem Soc (2006) 2.09
Simulation of pore formation in lipid bilayers by mechanical stress and electric fields. J Am Chem Soc (2003) 2.00
The mechanism of vesicle fusion as revealed by molecular dynamics simulations. J Am Chem Soc (2003) 1.83
The Role of histidine residues in low-pH-mediated viral membrane fusion. Structure (2006) 1.75
Toroidal pores formed by antimicrobial peptides show significant disorder. Biochim Biophys Acta (2008) 1.73
Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci (2004) 1.66
Molecular dynamics simulations of hydrophilic pores in lipid bilayers. Biophys J (2004) 1.65
Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: a molecular dynamics study. Proc Natl Acad Sci U S A (2002) 1.64
Basic ingredients of free energy calculations: a review. J Comput Chem (2010) 1.60
Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chem Phys Lipids (2005) 1.56
Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles. J Am Chem Soc (2003) 1.56
A new force field for simulating phosphatidylcholine bilayers. J Comput Chem (2010) 1.43
Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry. Proc Natl Acad Sci U S A (2007) 1.42
Structure, initial excited-state relaxation, and energy storage of rhodopsin resolved at the multiconfigurational perturbation theory level. Proc Natl Acad Sci U S A (2004) 1.40
Calculation of the free energy of solvation for neutral analogs of amino acid side chains. J Comput Chem (2002) 1.36
Simulation of MscL gating in a bilayer under stress. Biophys J (2003) 1.31
Reproducible polypeptide folding and structure prediction using molecular dynamics simulations. J Mol Biol (2005) 1.28
Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins (2008) 1.25
Analysis and evaluation of channel models: simulations of alamethicin. Biophys J (2002) 1.25
Does isoprene protect plant membranes from thermal shock? A molecular dynamics study. Biochim Biophys Acta (2006) 1.21
Molecular view of hexagonal phase formation in phospholipid membranes. Biophys J (2004) 1.21
Probing the rhodopsin cavity with reduced retinal models at the CASPT2//CASSCF/AMBER level of theory. J Am Chem Soc (2003) 1.18
Histidine protonation and the activation of viral fusion proteins. Biochem Soc Trans (2008) 1.15
Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayers. Biophys J (2009) 1.14
Entropy calculations on the molten globule state of a protein: side-chain entropies of alpha-lactalbumin. Proteins (2002) 1.13
3₁₀-helix conformation facilitates the transition of a voltage sensor S4 segment toward the down state. Biophys J (2011) 1.11
The color of rhodopsins at the ab initio multiconfigurational perturbation theory resolution. Proc Natl Acad Sci U S A (2006) 1.11
Synthesis, structure, and magnetic properties of an antiferromagnetic spin-ladder complex: bis(2,3-dimethylpyridinium) tetrabromocuprate. J Am Chem Soc (2007) 1.11
Molecular simulation as an aid to experimentalists. Curr Opin Struct Biol (2008) 1.09
Ion transport across transmembrane pores. Biophys J (2007) 1.09
Comparative study of generalized Born models: protein dynamics. Proc Natl Acad Sci U S A (2005) 1.08
Monolayer ice. Phys Rev Lett (2003) 1.07
Properties of the emitting state of the green fluorescent protein resolved at the CASPT2//CASSCF/CHARMM level. J Am Chem Soc (2005) 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
Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detail. J Am Chem Soc (2004) 1.06
A dynamic pharmacophore drives the interaction between Psalmotoxin-1 and the putative drug target acid-sensing ion channel 1a. Mol Pharmacol (2011) 1.05
Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin. J Am Chem Soc (2003) 1.04
Ultrafast deactivation channel for thymine dimerization. J Am Chem Soc (2007) 1.04
Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study. Proteins (2003) 1.03
Folding and stability of the three-stranded beta-sheet peptide Betanova: insights from molecular dynamics simulations. Proteins (2002) 1.03
Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent. J Chem Phys (2007) 1.02
Structure, spectroscopy, and spectral tuning of the gas-phase retinal chromophore: the beta-ionone "handle" and alkyl group effect. J Phys Chem A (2005) 1.02
Ultrafast deactivation of an excited cytosine-guanine base pair in DNA. J Am Chem Soc (2007) 1.02
Molecular structure of the lecithin ripple phase. Proc Natl Acad Sci U S A (2005) 1.02
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
Molecular dynamics simulations as a tool for improving protein stability. Protein Eng (2002) 0.99
Application of mean field boundary potentials in simulations of lipid vesicles. J Phys Chem B (2008) 0.98
Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore. Proteins (2002) 0.98
Chromophore protonation state controls photoswitching of the fluoroprotein asFP595. PLoS Comput Biol (2008) 0.96
Coherent ultrafast torsional motion and isomerization of a biomimetic dipolar photoswitch. Phys Chem Chem Phys (2010) 0.96
Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not biologically feasible. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.96
Counterion controlled photoisomerization of retinal chromophore models: a computational investigation. J Am Chem Soc (2004) 0.95
Cyclooctatetraene computational photo- and thermal chemistry: a reactivity model for conjugated hydrocarbons. J Am Chem Soc (2002) 0.94
Molecular dynamics study of the folding of hydrophobin SC3 at a hydrophilic/hydrophobic interface. Biophys J (2002) 0.94
Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structures. Protein Sci (2004) 0.93
Structure of the intersection space associated with ZIE photoisomerization of retinal in rhodopsin proteins. Faraday Discuss (2004) 0.93
Calculation of the redox potential of the protein azurin and some mutants. Chembiochem (2005) 0.93
The Cys3-Cys4 loop of the hydrophobin EAS is not required for rodlet formation and surface activity. J Mol Biol (2008) 0.93
The ultrafast photoisomerizations of rhodopsin and bathorhodopsin are modulated by bond length alternation and HOOP driven electronic effects. J Am Chem Soc (2011) 0.92
The molecular mechanism of thermal noise in rod photoreceptors. Science (2012) 0.92
Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes. Proteins (2002) 0.91
Arginine52 controls the photoisomerization process in photoactive yellow protein. J Am Chem Soc (2008) 0.91
Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes. J Comput Aided Mol Des (2010) 0.90
Ground and excited state CASPT2 geometry optimizations of small organic molecules. J Comput Chem (2003) 0.90
Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. J Comput Aided Mol Des (2014) 0.89
Using the computer to understand the chemistry of conical intersections. Photochem Photobiol Sci (2011) 0.89
Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail. J Am Chem Soc (2006) 0.89
Reaction path analysis of the "tunable" photoisomerization selectivity of free and locked retinal chromophores. J Am Chem Soc (2002) 0.89
Factors that affect the degree of twist in beta-sheet structures: a molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide. J Phys Chem B (2009) 0.89
Intramolecular charge transfer in 4-aminobenzonitriles does not necessarily need the twist. J Am Chem Soc (2005) 0.88
A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides. J Biomol NMR (2002) 0.87
Charge group partitioning in biomolecular simulation. J Comput Biol (2013) 0.87
Turning the growth hormone receptor on: evidence that hormone binding induces subunit rotation. Proteins (2010) 0.86
Simulation studies of pore and domain formation in a phospholipid monolayer. J Chem Phys (2005) 0.86
Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models. Proteins (2012) 0.86
SHAKE parallelization. Eur Phys J Spec Top (2011) 0.86
Conformational polymorphism of the PrP106-126 peptide in different environments: a molecular dynamics study. J Phys Chem B (2006) 0.85
Weak, strong, and coherent regimes of Fröhlich condensation and their applications to terahertz medicine and quantum consciousness. Proc Natl Acad Sci U S A (2009) 0.85
The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: a molecular dynamics study. Proteins (2008) 0.85
Effect of methyl-branched fatty acids on the structure of lipid bilayers. J Phys Chem B (2014) 0.85
A fast photoswitch for minimally perturbed peptides: investigation of the trans-->cis photoisomerization of N-methylthioacetamide. J Am Chem Soc (2004) 0.85
Incorporating the effect of ionic strength in free energy calculations using explicit ions. J Comput Chem (2005) 0.85
The free energy barrier for arginine gating charge translation is altered by mutations in the voltage sensor domain. PLoS One (2012) 0.85
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations. J Comput Chem (2011) 0.84
On the characterization of host-guest complexes: surface tension, calorimetry, and molecular dynamics of cyclodextrins with a non-ionic surfactant. J Phys Chem B (2007) 0.84
Competing adsorption between hydrated peptides and water onto metal surfaces: from electronic to conformational properties. J Am Chem Soc (2008) 0.84
Ion pairing in aqueous electrolyte solutions with biologically relevant anions. J Phys Chem B (2011) 0.84
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions. J Comput Chem (2006) 0.84
Excited-state singlet manifold and oscillatory features of a nonatetraeniminium retinal chromophore model. J Am Chem Soc (2003) 0.83