Published in Structure on July 01, 2002
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
Molecular dynamics and protein function. Proc Natl Acad Sci U S A (2005) 4.70
Torque generation and elastic power transmission in the rotary F(O)F(1)-ATPase. Nature (2009) 2.72
Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase. Biophys J (2004) 2.33
On the structure of the stator of the mitochondrial ATP synthase. EMBO J (2006) 1.90
Structure of the mitochondrial ATP synthase by electron cryomicroscopy. EMBO J (2003) 1.84
Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase. Proc Natl Acad Sci U S A (2006) 1.65
Domain compliance and elastic power transmission in rotary F(O)F(1)-ATPase. Proc Natl Acad Sci U S A (2008) 1.57
Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL. PLoS Comput Biol (2009) 1.50
How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase. Proc Natl Acad Sci U S A (2008) 1.50
The missing link between thermodynamics and structure in F1-ATPase. Proc Natl Acad Sci U S A (2003) 1.48
New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. Curr Protein Pept Sci (2004) 1.41
Correlation between the conformational states of F1-ATPase as determined from its crystal structure and single-molecule rotation. Proc Natl Acad Sci U S A (2008) 1.25
A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F1-ATPase. Proc Natl Acad Sci U S A (2003) 1.22
Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -ATPase. Biophys J (2004) 1.21
A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL. Biophys J (2006) 1.20
Phosphate release coupled to rotary motion of F1-ATPase. Proc Natl Acad Sci U S A (2013) 1.18
Functional rotation of the transporter AcrB: insights into drug extrusion from simulations. PLoS Comput Biol (2010) 1.15
Structure-based model of the stepping motor of PcrA helicase. Biophys J (2006) 1.12
Stiffness of γ subunit of F(1)-ATPase. Eur Biophys J (2010) 1.12
Elastic energy storage in beta-sheets with application to F1-ATPase. Eur Biophys J (2003) 1.10
Allosteric transition pathways in the lactose repressor protein core domains: asymmetric motions in a homodimer. Protein Sci (2003) 1.03
Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability. Biophys J (2004) 1.03
Making ATP. Proc Natl Acad Sci U S A (2005) 1.02
The human cytomegalovirus UL44 C clamp wraps around DNA. Structure (2008) 1.02
F1F0-ATP synthases of alkaliphilic bacteria: lessons from their adaptations. Biochim Biophys Acta (2010) 1.00
The unbinding of ATP from F1-ATPase. Biophys J (2003) 1.00
Role of the DELSEED loop in torque transmission of F1-ATPase. Biophys J (2012) 0.97
Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin. J Phys Chem B (2012) 0.95
Conformational dynamics of the F1-ATPase beta-subunit: a molecular dynamics study. Biophys J (2003) 0.93
Trapping the ATP binding state leads to a detailed understanding of the F1-ATPase mechanism. Proc Natl Acad Sci U S A (2014) 0.89
Theoretical analysis of twist/bend ratio and mechanical moduli of bacterial flagellar hook and filament. Biophys J (2004) 0.88
Simulating movement of tRNA through the ribosome during hybrid-state formation. J Chem Phys (2013) 0.87
End-point targeted molecular dynamics: large-scale conformational changes in potassium channels. Biophys J (2008) 0.87
A direct coupling between global and internal motions in a single domain protein? MD investigation of extreme scenarios. Biophys J (2011) 0.85
Rate of hydrolysis in ATP synthase is fine-tuned by α-subunit motif controlling active site conformation. Proc Natl Acad Sci U S A (2013) 0.83
Domain motion of individual F1-ATPase β-subunits during unbiased molecular dynamics simulations. J Phys Chem A (2011) 0.83
Investigation of pathways for the low-pH conformational transition in influenza hemagglutinin. Biophys J (2003) 0.82
Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations. Top Curr Chem (2013) 0.81
Double-lock ratchet mechanism revealing the role of alphaSER-344 in FoF1 ATP synthase. Proc Natl Acad Sci U S A (2011) 0.81
Identification of the Conformational transition pathway in PIP2 Opening Kir Channels. Sci Rep (2015) 0.78
A computational analysis of ATP binding of SV40 large tumor antigen helicase motor. PLoS Comput Biol (2009) 0.78
An improved strategy for generating forces in steered molecular dynamics: the mechanical unfolding of titin, e2lip3 and ubiquitin. PLoS One (2010) 0.78
Ligand-induced changes in the conformational stability and flexibility of glutamate dehydrogenase and their role in catalysis and regulation. Protein Sci (2010) 0.78
Does F1-ATPase have a catalytic site that preferentially binds MgADP? FEBS Lett (2006) 0.78
Equilibrium sampling for biomolecules under mechanical tension. Biophys J (2010) 0.77
Mutations on the N-terminal edge of the DELSEED loop in either the α or β subunit of the mitochondrial F1-ATPase enhance ATP hydrolysis in the absence of the central γ rotor. Eukaryot Cell (2013) 0.77
Computational study of correlated domain motions in the AcrB efflux transporter. Biomed Res Int (2015) 0.76
Importance of water entropy in rotation mechanism of F1-ATPase. Biophysics (Nagoya-shi) (2011) 0.75
A molecular dynamic analysis of interaction between the gamma-subunit and a C-terminal fragment of the beta-subunit of F1-ATPase. Dokl Biochem Biophys (2010) 0.75
Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr (2011) 67.55
iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM. Acta Crystallogr D Biol Crystallogr (2011) 18.13
Structure of a beta1-adrenergic G-protein-coupled receptor. Nature (2008) 11.97
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature (2007) 5.78
Intrinsic motions along an enzymatic reaction trajectory. Nature (2007) 5.53
Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation. Nature (2011) 4.60
The structural basis for agonist and partial agonist action on a β(1)-adrenergic receptor. Nature (2011) 4.31
How enzymes work: analysis by modern rate theory and computer simulations. Science (2004) 4.30
Allostery and cooperativity revisited. Protein Sci (2008) 3.70
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature (2005) 3.67
Structure of the rotor of the V-Type Na+-ATPase from Enterococcus hirae. Science (2005) 3.46
A Src-like inactive conformation in the abl tyrosine kinase domain. PLoS Biol (2006) 3.40
Bovine complex I is a complex of 45 different subunits. J Biol Chem (2006) 3.01
Hidden complexity of free energy surfaces for peptide (protein) folding. Proc Natl Acad Sci U S A (2004) 2.65
Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase. J Mol Biol (2005) 2.59
Bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria. Proc Natl Acad Sci U S A (2010) 2.50
The nuclear encoded subunits of complex I from bovine heart mitochondria. Biochim Biophys Acta (2003) 2.37
A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase. Biophys J (2002) 2.26
Autoindexing diffraction images with iMosflm. Acta Crystallogr D Biol Crystallogr (2013) 2.25
Ground state structure of F1-ATPase from bovine heart mitochondria at 1.9 A resolution. J Biol Chem (2007) 2.19
Ectopic beta-chain of ATP synthase is an apolipoprotein A-I receptor in hepatic HDL endocytosis. Nature (2003) 2.14
Protein structural variation in computational models and crystallographic data. Structure (2007) 2.13
Mitochondrial quality control mediated by PINK1 and Parkin: links to parkinsonism. Cold Spring Harb Perspect Biol (2012) 2.10
The structure of bovine F1-ATPase inhibited by ADP and beryllium fluoride. EMBO J (2004) 2.08
Analysis of the subunit composition of complex I from bovine heart mitochondria. Mol Cell Proteomics (2003) 2.06
Free energy simulations come of age: protein-ligand recognition. Acc Chem Res (2002) 2.04
Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. J Mol Biol (2002) 2.00
The crystal structure of murine p97/VCP at 3.6A. J Struct Biol (2003) 1.98
Molecular dynamics simulations of biomolecules. Acc Chem Res (2002) 1.95
A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. J Mol Biol (2004) 1.92
The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis. Structure (2010) 1.91
On the structure of the stator of the mitochondrial ATP synthase. EMBO J (2006) 1.90
Novel features of the rotary catalytic mechanism revealed in the structure of yeast F1 ATPase. EMBO J (2006) 1.89
Structure of the mitochondrial ATP synthase by electron cryomicroscopy. EMBO J (2003) 1.84
Structure of the adenosine A(2A) receptor bound to an engineered G protein. Nature (2016) 1.84
Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B (2006) 1.83
The structure of bovine F1-ATPase in complex with its regulatory protein IF1. Nat Struct Biol (2003) 1.78
The structure of the membrane extrinsic region of bovine ATP synthase. Proc Natl Acad Sci U S A (2009) 1.77
Mechanism of inhibition of bovine F1-ATPase by resveratrol and related polyphenols. Proc Natl Acad Sci U S A (2007) 1.75
Optimal estimates of free energies from multistate nonequilibrium work data. Phys Rev Lett (2006) 1.73
Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY). Proteins (2006) 1.67
How the regulatory protein, IF(1), inhibits F(1)-ATPase from bovine mitochondria. Proc Natl Acad Sci U S A (2007) 1.67
Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme. Nature (2009) 1.67
How azide inhibits ATP hydrolysis by the F-ATPases. Proc Natl Acad Sci U S A (2006) 1.65
Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data. Biophys J (2006) 1.62
Two distinct conformations of helix 6 observed in antagonist-bound structures of a beta1-adrenergic receptor. Proc Natl Acad Sci U S A (2011) 1.59
Kinesin's cover-neck bundle folds forward to generate force. Proc Natl Acad Sci U S A (2008) 1.57
Crystal structures of a stabilized β1-adrenoceptor bound to the biased agonists bucindolol and carvedilol. Structure (2012) 1.55
A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase. Cell (2005) 1.55
Application of the diffusion-collision model to the folding of three-helix bundle proteins. J Mol Biol (2002) 1.53
Force generation in kinesin hinges on cover-neck bundle formation. Structure (2008) 1.53
The AAA+ protein ATAD3 has displacement loop binding properties and is involved in mitochondrial nucleoid organization. J Cell Biol (2007) 1.53
Kinetic control of dimer structure formation in amyloid fibrillogenesis. Proc Natl Acad Sci U S A (2004) 1.52
The role of sequence and structure in protein folding kinetics; the diffusion-collision model applied to proteins L and G. Structure (2004) 1.51
How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase. Proc Natl Acad Sci U S A (2008) 1.50
New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow. J Phys Chem B (2013) 1.48
Determination of a transition state at atomic resolution from protein engineering data. J Mol Biol (2002) 1.47
Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor. Biochemistry (2008) 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
The phosphorylation of subunits of complex I from bovine heart mitochondria. J Biol Chem (2004) 1.43
What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis. J Mol Biol (2005) 1.40
DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput (2012) 1.40
Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. PLoS Comput Biol (2006) 1.39
Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method. J Chem Phys (2005) 1.38
Why protein R-factors are so large: a self-consistent analysis. Proteins (2002) 1.36
Motions and negative cooperativity between p97 domains revealed by cryo-electron microscopy and quantised elastic deformational model. J Mol Biol (2003) 1.36
Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature (2010) 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
Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI. J Chem Phys (2011) 1.34
Product-assisted catalysis in base-excision DNA repair. Nat Struct Biol (2003) 1.34
Identification of the mitochondrial glutamate transporter. Bacterial expression, reconstitution, functional characterization, and tissue distribution of two human isoforms. J Biol Chem (2002) 1.33
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J Chem Phys (2005) 1.33
Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors. Proc Natl Acad Sci U S A (2006) 1.32
One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers. J Phys Chem B (2006) 1.32
pKa of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling. J Phys Chem B (2008) 1.32
Pi release from myosin: a simulation analysis of possible pathways. Structure (2010) 1.31
Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence. J Chem Phys (2004) 1.31
Application of elastic network models to proteins in the crystalline state. Biophys J (2009) 1.30
Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants. J Am Chem Soc (2002) 1.30
PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis. Proc Natl Acad Sci U S A (2010) 1.30
Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis. Proteins (2009) 1.29
Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange. J Am Chem Soc (2003) 1.27
Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes. J Comput Chem (2001) 1.27
Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition. Proteins (2005) 1.27
The origin of protein sidechain order parameter distributions. J Am Chem Soc (2004) 1.25
DNA polymorphism: a comparison of force fields for nucleic acids. Biophys J (2003) 1.25
Lysine 43 is trimethylated in subunit C from bovine mitochondrial ATP synthase and in storage bodies associated with batten disease. J Biol Chem (2004) 1.23
pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols. J Phys Chem B (2005) 1.23