Published in J Am Chem Soc on May 27, 2009
DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput (2012) 1.40
Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water. J Phys Chem B (2011) 0.90
Density functional tight binding: values of semi-empirical methods in an ab initio era. Phys Chem Chem Phys (2014) 0.89
Structural model of channelrhodopsin. J Biol Chem (2012) 0.88
Conversion of a light-driven proton pump into a light-gated ion channel. Sci Rep (2015) 0.83
VMD: visual molecular dynamics. J Mol Graph (1996) 117.02
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
Structure of bacteriorhodopsin at 1.55 A resolution. J Mol Biol (1999) 8.17
The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. J Mol Biol (2004) 7.38
Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 A resolution. Structure (1999) 2.50
Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex. Proc Natl Acad Sci U S A (1998) 2.48
Structural alterations for proton translocation in the M state of wild-type bacteriorhodopsin. Nature (2000) 2.37
Glutamic acid 204 is the terminal proton release group at the extracellular surface of bacteriorhodopsin. J Biol Chem (1995) 2.36
Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy. Nature (2005) 2.31
Kinetic and spectroscopic evidence for an irreversible step between deprotonation and reprotonation of the Schiff base in the bacteriorhodopsin photocycle. Biochemistry (1991) 2.23
Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B (2006) 1.83
Determination of retinal chromophore structure in bacteriorhodopsin with resonance Raman spectroscopy. J Membr Biol (1985) 1.83
A model-independent approach to assigning bacteriorhodopsin's intramolecular reactions to photocycle intermediates. Biophys J (1993) 1.77
Titration of aspartate-85 in bacteriorhodopsin: what it says about chromophore isomerization and proton release. Biophys J (1996) 1.74
Molecular mechanism of spectral tuning in sensory rhodopsin II. Biochemistry (2001) 1.72
Replacement of leucine-93 by alanine or threonine slows down the decay of the N and O intermediates in the photocycle of bacteriorhodopsin: implications for proton uptake and 13-cis-retinal----all-trans-retinal reisomerization. Proc Natl Acad Sci U S A (1991) 1.69
Bacteriorhodopsin's intramolecular proton-release pathway consists of a hydrogen-bonded network. Biochemistry (1998) 1.69
Specific damage induced by X-ray radiation and structural changes in the primary photoreaction of bacteriorhodopsin. J Mol Biol (2002) 1.52
The two pKa's of aspartate-85 and control of thermal isomerization and proton release in the arginine-82 to lysine mutant of bacteriorhodopsin. Biochemistry (1995) 1.52
Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal. J Mol Biol (2002) 1.51
Structural changes during the formation of early intermediates in the bacteriorhodopsin photocycle. Biophys J (2002) 1.49
Protein conformational changes in the bacteriorhodopsin photocycle. J Mol Biol (1999) 1.45
Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction. J Phys Chem A (2007) 1.44
Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc (2006) 1.43
Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle. Biophys J (2001) 1.36
Proton binding within a membrane protein by a protonated water cluster. Proc Natl Acad Sci U S A (2005) 1.36
Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis. J Comput Chem (2003) 1.35
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J Chem Phys (2005) 1.33
pKa of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling. J Phys Chem B (2008) 1.32
In situ determination of transient pKa changes of internal amino acids of bacteriorhodopsin by using time-resolved attenuated total reflection Fourier-transform infrared spectroscopy. Proc Natl Acad Sci U S A (1999) 1.28
Crystal structure of the L intermediate of bacteriorhodopsin: evidence for vertical translocation of a water molecule during the proton pumping cycle. J Mol Biol (2004) 1.23
Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin. Biophys J (2000) 1.23
Molecular dynamics simulation of bacteriorhodopsin's photoisomerization using ab initio forces for the excited chromophore. Biophys J (2003) 1.22
The tertiary structural changes in bacteriorhodopsin occur between M states: X-ray diffraction and Fourier transform infrared spectroscopy. EMBO J (1997) 1.20
Calculating absorption shifts for retinal proteins: computational challenges. J Phys Chem B (2005) 1.18
What is so special about Arg 55 in the catalysis of cyclophilin A? insights from hybrid QM/MM simulations. J Am Chem Soc (2003) 1.18
Crystallographic structure of the retinal and the protein after deprotonation of the Schiff base: the switch in the bacteriorhodopsin photocycle. J Mol Biol (2002) 1.16
Structures and spectral signatures of protonated water networks in bacteriorhodopsin. Proc Natl Acad Sci U S A (2007) 1.15
A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method. J Phys Chem B (2005) 1.15
Kinetic and thermodynamic study of the bacteriorhodopsin photocycle over a wide pH range. Biophys J (1998) 1.13
Electron diffraction studies of light-induced conformational changes in the Leu-93 --> Ala bacteriorhodopsin mutant. Proc Natl Acad Sci U S A (1997) 1.10
"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. J Am Chem Soc (2006) 1.09
Crystal structure of the D85S mutant of bacteriorhodopsin: model of an O-like photocycle intermediate. J Mol Biol (2001) 1.07
Calculation of proton transfers in Bacteriorhodopsin bR and M intermediates. Biochemistry (2003) 1.03
Crystal structures of acid blue and alkaline purple forms of bacteriorhodopsin. J Mol Biol (2005) 1.02
Tight Asp-85--Thr-89 association during the pump switch of bacteriorhodopsin. Proc Natl Acad Sci U S A (2001) 1.01
Key role of electrostatic interactions in bacteriorhodopsin proton transfer. J Am Chem Soc (2004) 1.00
Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proc Natl Acad Sci U S A (2008) 0.98
CD spectrum of bacteriorhodopsin: Best evidence against exciton model. Biophys J (1991) 0.96
The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all. Biochim Biophys Acta (2008) 0.96
Chromophore distortions in the bacteriorhodopsin photocycle: evolution of the H-C14-C15-H dihedral angle measured by solid-state NMR. Biochemistry (2002) 0.95
Infrared methods for monitoring the protonation state of carboxylic amino acids in the photocycle of bacteriorhodopsin. Biochemistry (Mosc) (2001) 0.94
Temperature and pH sensitivity of the O(640) intermediate of the bacteriorhodopsin photocycle. Biophys J (1992) 0.92
Functional specificities of methylglyoxal synthase and triosephosphate isomerase: a combined QM/MM analysis. J Am Chem Soc (2002) 0.92
Key role of active-site water molecules in bacteriorhodopsin proton-transfer reactions. J Phys Chem B (2008) 0.91
Fourier transform infrared spectra of a late intermediate of the bacteriorhodopsin photocycle suggest transient protonation of Asp-212. Biochemistry (1999) 0.91
Is there an excitonic interaction or antenna system in bacteriorhodopsin? Proc Natl Acad Sci U S A (1989) 0.91
Role of hydrogen-bond network in energy storage of bacteriorhodopsin's light-driven proton pump revealed by ab initio normal-mode analysis. J Am Chem Soc (2004) 0.90
Effect of polarization on the opsin shift in rhodopsins. 1. A combined QM/QM/MM model for bacteriorhodopsin and pharaonis sensory rhodopsin II. J Phys Chem B (2008) 0.89
Effect of polarization on the opsin shift in rhodopsins. 2. Empirical polarization models for proteins. J Phys Chem B (2008) 0.88
Relationship of retinal configuration and internal proton transfer at the end of the bacteriorhodopsin photocycle. Biochemistry (1996) 0.88
Partitioning of free energy gain between the photoisomerized retinal and the protein in bacteriorhodopsin. Biochemistry (1998) 0.87
Time-resolved FT-IR spectroscopic investigation of the pH-dependent proton transfer reactions in the E194Q mutant of bacteriorhodopsin. Biochem Biophys Res Commun (2001) 0.87
The vibrational spectra of protonated water clusters: a benchmark for self-consistent-charge density-functional tight binding. J Chem Phys (2007) 0.85
Time-resolved microspectroscopy on a single crystal of bacteriorhodopsin reveals lattice-induced differences in the photocycle kinetics. Biophys J (2006) 0.84
Tuning of retinal twisting in bacteriorhodopsin controls the directionality of the early photocycle steps. J Phys Chem B (2005) 0.84
Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM method. J Comput Chem (2006) 0.83
Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: a theoretical analysis of structural elements. J Struct Biol (2006) 0.81
Electron paramagnetic resonance study of structural changes in the O photointermediate of bacteriorhodopsin. J Mol Biol (2006) 0.81
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (2013) 11.01
Effectiveness of the global protected area network in representing species diversity. Nature (2004) 10.66
Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res (2004) 10.40
The status of the world's land and marine mammals: diversity, threat, and knowledge. Science (2008) 8.03
The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. J Mol Biol (2004) 7.38
The value of the IUCN Red List for conservation. Trends Ecol Evol (2005) 4.25
Conservation. Protected areas and effective biodiversity conservation. Science (2013) 3.42
Fragmentation pathways of protonated peptides. Mass Spectrom Rev (2005) 3.36
The genetic basis for bacterial mercury methylation. Science (2013) 2.87
Pinpointing and preventing imminent extinctions. Proc Natl Acad Sci U S A (2005) 2.64
Conversion of channelrhodopsin into a light-gated chloride channel. Science (2014) 2.56
Protecting important sites for biodiversity contributes to meeting global conservation targets. PLoS One (2012) 2.50
Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states. J Chem Phys (2007) 2.23
Is the first hydration shell of lysozyme of higher density than bulk water? Proc Natl Acad Sci U S A (2002) 2.19
Global habitat suitability models of terrestrial mammals. Philos Trans R Soc Lond B Biol Sci (2011) 2.18
Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proc Natl Acad Sci U S A (2011) 1.96
Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev (2013) 1.93
Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B (2006) 1.83
GOPET: a tool for automated predictions of Gene Ontology terms. BMC Bioinformatics (2006) 1.75
Structural mechanism of the recovery stroke in the myosin molecular motor. Proc Natl Acad Sci U S A (2005) 1.66
Translational hydration water dynamics drives the protein glass transition. Biophys J (2003) 1.63
ESTAnnotator: A tool for high throughput EST annotation. Nucleic Acids Res (2003) 1.56
Applying Support Vector Machines for Gene Ontology based gene function prediction. BMC Bioinformatics (2004) 1.47
Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction. J Phys Chem A (2007) 1.44
Principal components of the protein dynamical transition. Phys Rev Lett (2003) 1.43
Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc (2006) 1.43
Fluorescence quenching of dyes by tryptophan: interactions at atomic detail from combination of experiment and computer simulation. J Am Chem Soc (2003) 1.42
DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput (2012) 1.40
SASSIM: a method for calculating small-angle X-ray and neutron scattering and the associated molecular envelope from explicit-atom models of solvated proteins. Acta Crystallogr D Biol Crystallogr (2002) 1.36
A task framework for the web interface W2H. Bioinformatics (2003) 1.33
Structural basis of cellulosome efficiency explored by small angle X-ray scattering. J Biol Chem (2005) 1.32
Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian. Biophys J (2007) 1.30
Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations. J Am Chem Soc (2008) 1.30
Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. J Phys Chem A (2007) 1.27
Warfare in biodiversity hotspots. Conserv Biol (2009) 1.26
Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2010) 1.26
The structural coupling between ATPase activation and recovery stroke in the myosin II motor. Structure (2007) 1.22
Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction? J Comput Chem (2002) 1.21
In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions. J Am Chem Soc (2011) 1.20
Direct determination of vibrational density of states change on ligand binding to a protein. Phys Rev Lett (2004) 1.20
Mechanism of primary proton transfer in bacteriorhodopsin. Structure (2004) 1.17
Towards understanding the tandem mass spectra of protonated oligopeptides. 1: mechanism of amide bond cleavage. J Am Soc Mass Spectrom (2004) 1.13
Automated computation of low-energy pathways for complex rearrangements in proteins: application to the conformational switch of Ras p21. Proteins (2005) 1.12
Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease. Biophys J (2005) 1.10
Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties. Biophys J (2002) 1.09
The alpha helix dipole: screened out? Structure (2005) 1.09
Simulating water with the self-consistent-charge density functional tight binding method: from molecular clusters to the liquid state. J Phys Chem A (2007) 1.09
"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. J Am Chem Soc (2006) 1.09
Mechanism and kinetics of peptide partitioning into membranes from all-atom simulations of thermostable peptides. J Am Chem Soc (2010) 1.09
Sequence-scrambling fragmentation pathways of protonated peptides. J Am Chem Soc (2008) 1.08
The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor. J Mol Biol (2006) 1.08
Early changes in experimental osteoarthritis using the Pond-Nuki dog model: technical procedure and initial results of in vivo MR imaging. Eur Radiol (2004) 1.08
Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. Proc Natl Acad Sci U S A (2007) 1.07
Improvement in left ventricular remodeling by the endothelial nitric oxide synthase enhancer AVE9488 after experimental myocardial infarction. Circulation (2008) 1.07
Differential effects of cholesterol, ergosterol and lanosterol on a dipalmitoyl phosphatidylcholine membrane: a molecular dynamics simulation study. J Phys Chem B (2007) 1.05
SERpredict: detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements. BMC Genet (2007) 1.05
Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics. J Phys Chem B (2005) 1.05
Complete, accurate, mammalian phylogenies aid conservation planning, but not much. Philos Trans R Soc Lond B Biol Sci (2011) 1.04
Role of histone tails in structural stability of the nucleosome. PLoS Comput Biol (2011) 1.04
Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog. Biotechnol Biofuels (2012) 1.04
Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer. Phys Chem Chem Phys (2005) 1.04
A molecular mechanics force field for biologically important sterols. J Comput Chem (2005) 1.03
Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. J Chem Phys (2011) 1.03
Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization. J Chem Theory Comput (2008) 1.03
Spectroscopic and theoretical evidence for oxazolone ring formation in collision-induced dissociation of peptides. J Am Chem Soc (2005) 1.01
What is the risk of stress risers for interprosthetic fractures of the femur? A biomechanical analysis. Int Orthop (2012) 1.01
Key role of electrostatic interactions in bacteriorhodopsin proton transfer. J Am Chem Soc (2004) 1.00
Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study. Biophys J (2012) 1.00
Biomechanical evaluation of 3 stabilization methods on acromioclavicular joint dislocations. Am J Sports Med (2013) 0.99
Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism. Biochemistry (2006) 0.99
Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data. J Chem Phys (2005) 0.98
Proton-driven amide bond-cleavage pathways of gas-phase peptide ions lacking mobile protons. J Am Chem Soc (2009) 0.98
Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proc Natl Acad Sci U S A (2008) 0.98
Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers. J Comput Chem (2010) 0.98
Neutron frequency windows and the protein dynamical transition. Biophys J (2004) 0.98
Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns. Proteins (2007) 0.98
Internal fixation of femoral neck fractures with posterior comminution: a biomechanical comparison of DHS® and Intertan nail®. Int Orthop (2011) 0.97
Energy resolution and dynamical heterogeneity effects on elastic incoherent neutron scattering from molecular systems. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.96
The effect of the initial water of hydration on the energetics, structures, and H/D exchange mechanism of a family of pentapeptides: an experimental and theoretical study. J Am Chem Soc (2003) 0.96
Towards understanding some ion intensity relationships for the tandem mass spectra of protonated peptides. Rapid Commun Mass Spectrom (2002) 0.96
Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proc Natl Acad Sci U S A (2011) 0.96
Combined quantum chemical and RRKM modeling of the main fragmentation pathways of protonated GGG. II. Formation of b(2), y(1), and y(2) ions. Rapid Commun Mass Spectrom (2002) 0.96
Towards understanding the tandem mass spectra of protonated oligopeptides. 2: The proline effect in collision-induced dissociation of protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp). J Am Soc Mass Spectrom (2011) 0.96
Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations. J Am Chem Soc (2009) 0.95
Simulations of the myosin II motor reveal a nucleotide-state sensing element that controls the recovery stroke. J Mol Biol (2006) 0.95
Protein dynamics and stability: the distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scattering. Biophys J (2008) 0.95
Temperature-dependent dynamical transitions of different classes of amino acid residue in a globular protein. J Am Chem Soc (2012) 0.95
Reorientation and dimerization of the membrane-bound antimicrobial peptide PGLa from microsecond all-atom MD simulations. Biophys J (2012) 0.94
Kinetics of proton release and uptake by channelrhodopsin-2. FEBS Lett (2012) 0.94
11-cis-retinal protonated Schiff base: influence of the protein environment on the geometry of the rhodopsin chromophore. Biochemistry (2002) 0.94