Published in Biophys J on July 01, 1995
Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys J (2004) 6.67
Simulation of the diffusional association of barnase and barstar. Biophys J (1997) 3.33
Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: adaptive finite element analysis. Biophys J (2004) 1.89
Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association. Biophys J (2010) 1.29
Rational stabilization of enzymes by computational redesign of surface charge-charge interactions. Proc Natl Acad Sci U S A (2009) 1.27
Surface plasmon resonance analysis of antifungal azoles binding to CYP3A4 with kinetic resolution of multiple binding orientations. Biochemistry (2006) 1.17
Fruitful and futile encounters along the association reaction between proteins. Biophys J (2009) 1.08
Brownian dynamics simulation of protein solutions: structural and dynamical properties. Biophys J (2010) 1.07
Differences in electrostatic properties at antibody-antigen binding sites: implications for specificity and cross-reactivity. Biophys J (2002) 1.03
Krylov subspace methods for computing hydrodynamic interactions in brownian dynamics simulations. J Chem Phys (2012) 1.02
Brownian dynamics simulations of protein folding: access to milliseconds time scale and beyond. Proc Natl Acad Sci U S A (1998) 0.99
A method for computing association rate constants of atomistically represented proteins under macromolecular crowding. Phys Biol (2012) 0.92
Bimolecular reaction simulation using Weighted Ensemble Brownian dynamics and the University of Houston Brownian Dynamics program. Biophys J (2000) 0.92
Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations. J Biomol NMR (2004) 0.91
The binding process of a nonspecific enzyme with DNA. Biophys J (2011) 0.90
Influence of static and dynamic bends on the birefringence decay profile of RNA helices: Brownian dynamics simulations. Biophys J (1997) 0.87
A Brownian dynamics study: the effect of a membrane environment on an electron transfer system. Biophys J (2004) 0.86
A modular treatment of molecular traffic through the active site of cholinesterase. Biophys J (1999) 0.82
On the importance of hydrodynamic interactions in lipid membrane formation. Biophys J (2013) 0.82
Diffusion of hydrophobin proteins in solution and interactions with a graphite surface. BMC Biophys (2011) 0.80
A molecule-centered method for accelerating the calculation of hydrodynamic interactions in Brownian dynamics simulations containing many flexible biomolecules. J Chem Theory Comput (2013) 0.80
Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes. J Chem Phys (2015) 0.79
Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems. Phys Rev X (2015) 0.78
Attractive hydration forces in DNA-dendrimer interactions on the nanometer scale. J Phys Chem B (2013) 0.77
Linking 3D and 2D binding kinetics of membrane proteins by multiscale simulations. Protein Sci (2014) 0.76
IMPORTANCE OF EXCLUDED VOLUME AND HYDRODYNAMIC INTERACTIONS ON MACROMOLECULAR DIFFUSION IN VIVO. Quantum Bioinform V (2011) (2013) 0.75
Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications. Q Rev Biophys (1981) 7.08
Hydrodynamic steering effects in protein association. Proc Natl Acad Sci U S A (1994) 2.09
The translational friction coefficient of proteins. Methods Enzymol (1979) 2.05
Simulation of enzyme-substrate encounter with gated active sites. Nat Struct Biol (1994) 1.93
Acetylcholinesterase: diffusional encounter rate constants for dumbbell models of ligand. Biophys J (1995) 1.87
On the validity of the kirkwood-riseman theory. Proc Natl Acad Sci U S A (1968) 0.95
Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A (2001) 42.14
Dynamics of folded proteins. Nature (1977) 7.82
The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J (1997) 7.64
Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J Struct Biol (1999) 5.71
Prediction of pH-dependent properties of proteins. J Mol Biol (1994) 4.99
The internal dynamics of globular proteins. CRC Crit Rev Biochem (1981) 4.59
Dynamics of proteins: elements and function. Annu Rev Biochem (1983) 4.56
Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin. J Mol Biol (1999) 4.50
The determinants of pKas in proteins. Biochemistry (1996) 3.45
Picosecond dynamics of tyrosine side chains in proteins. Biochemistry (1979) 3.35
Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry. J Mol Biol (1999) 3.19
Dynamical theory of activated processes in globular proteins. Proc Natl Acad Sci U S A (1982) 2.94
The hinge-bending mode in lysozyme. Nature (1976) 2.78
Conformation gating as a mechanism for enzyme specificity. Proc Natl Acad Sci U S A (1998) 2.61
Open "back door" in a molecular dynamics simulation of acetylcholinesterase. Science (1994) 2.37
Thermodynamics and kinetics of actin filament nucleation. Biophys J (2001) 2.34
Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin. J Biol Chem (1997) 2.31
Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models. Phys Rev Lett (2006) 2.20
Water and polypeptide conformations in the gramicidin channel. A molecular dynamics study. Biophys J (1989) 2.14
The structure of Sky1p reveals a novel mechanism for constitutive activity. Nat Struct Biol (2001) 2.10
Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study. Biophys Chem (1999) 2.07
Shedding light on the dark and weakly fluorescent states of green fluorescent proteins. Proc Natl Acad Sci U S A (1999) 1.97
How electrolyte shielding influences the electrical potential in transmembrane ion channels. Biophys J (1989) 1.97
Protein structural fluctuations during a period of 100 ps. Nature (1979) 1.96
Simulation of enzyme-substrate encounter with gated active sites. Nat Struct Biol (1994) 1.93
Coupling nonpolar and polar solvation free energies in implicit solvent models. J Chem Phys (2006) 1.91
Time-correlation analysis of simulated water motion in flexible and rigid gramicidin channels. Biophys J (1991) 1.91
Acetylcholinesterase: diffusional encounter rate constants for dumbbell models of ligand. Biophys J (1995) 1.87
Accommodating protein flexibility in computational drug design. Mol Pharmacol (2000) 1.84
Hinge-bending in L-arabinose-binding protein. The "Venus's-flytrap" model. J Biol Chem (1982) 1.80
Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme. Biophys J (1993) 1.80
Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase. Biophys J (2001) 1.78
Developing a dynamic pharmacophore model for HIV-1 integrase. J Med Chem (2000) 1.71
Acetylcholinesterase: electrostatic steering increases the rate of ligand binding. Biochemistry (1993) 1.69
Point charge distributions and electrostatic steering in enzyme/substrate encounter: Brownian dynamics of modified copper/zinc superoxide dismutases. Biochemistry (1990) 1.67
Diffusion-controlled enzymatic reactions. Methods Enzymol (1991) 1.66
Quasi-harmonic method for studying very low frequency modes in proteins. Biopolymers (1984) 1.64
Kinetic mechanism of end-to-end annealing of actin filaments. J Mol Biol (2001) 1.63
Molecular dynamics of ferrocytochrome c. Magnitude and anisotropy of atomic displacements. J Mol Biol (1981) 1.60
Annealing accounts for the length of actin filaments formed by spontaneous polymerization. Biophys J (1999) 1.58
Identification of protein oligomerization states by analysis of interface conservation. Proc Natl Acad Sci U S A (2001) 1.57
Molecular dynamics of ferrocytochrome c: anharmonicity of atomic displacements. Biopolymers (1982) 1.56
Gated binding of ligands to proteins. Nature (1981) 1.52
Dynamics of activated processes in globular proteins. Proc Natl Acad Sci U S A (1979) 1.47
Theoretical calculation of relative binding affinity in host-guest systems. Proc Natl Acad Sci U S A (1986) 1.46
Simulation of the diffusion-controlled reaction between superoxide and superoxide dismutase. II. Detailed models. Biopolymers (1988) 1.45
Self-organizing neural networks bridge the biomolecular resolution gap. J Mol Biol (1998) 1.45
Dewetting-controlled binding of ligands to hydrophobic pockets. Phys Rev Lett (2009) 1.42
Molecular dynamics computations and solid state nuclear magnetic resonance of the gramicidin cation channel. Biophys J (1991) 1.42
Electrostatic contributions to the stability of halophilic proteins. J Mol Biol (1998) 1.42
Analysis of synaptic transmission in the neuromuscular junction using a continuum finite element model. Biophys J (1998) 1.40
Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge. Biopolymers (1998) 1.33
Internal motions of antibody molecules. Nature (1977) 1.29
Multistep Brownian dynamics: application to short wormlike chains. Biopolymers (1984) 1.26
Electrostatic channeling in the bifunctional enzyme dihydrofolate reductase-thymidylate synthase. J Mol Biol (1996) 1.23
Internal mobility of ferrocytochrome c. Nature (1980) 1.23
Evidence for electrostatic channeling in a fusion protein of malate dehydrogenase and citrate synthase. Biochemistry (1996) 1.21
A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins. Biopolymers (1991) 1.20
Acetylcholinesterase: role of the enzyme's charge distribution in steering charged ligands toward the active site. Biopolymers (1996) 1.19
Simulation of charge-mutant acetylcholinesterases. Biochemistry (1995) 1.18
Molecular dynamics of mouse acetylcholinesterase complexed with huperzine A. Biopolymers (1999) 1.18
Poisson-Boltzmann analysis of the lambda repressor-operator interaction. Biophys J (1992) 1.17
Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient. Biophys J (2001) 1.15
Orientational steering in enzyme-substrate association: ionic strength dependence of hydrodynamic torque effects. Eur Biophys J (1996) 1.13
Phenylalanine transfer RNA: molecular dynamics simulation. Science (1984) 1.12
Mouse acetylcholinesterase unliganded and in complex with huperzine A: a comparison of molecular dynamics simulations. Biopolymers (1999) 1.12
Molecular dynamics of ferrocytochrome c. Nature (1980) 1.11
Correlation between rate of enzyme-substrate diffusional encounter and average Boltzmann factor around active site. Biopolymers (1998) 1.10
Computation of the dipole moments of proteins. Biophys J (1995) 1.08
Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers (2006) 1.08
Phosphorylation stabilizes the N-termini of alpha-helices. Biopolymers (1999) 1.07
Atomistic Brownian dynamics simulation of peptide phosphorylation. J Am Chem Soc (2001) 1.07
Modeling the electrophoresis of lysozyme. II. Inclusion of ion relaxation. Biophys J (1997) 1.06
Molecular dynamics studies on the HIV-1 integrase catalytic domain. Biophys J (1999) 1.06
Substrate concentration dependence of the diffusion-controlled steady-state rate constant. J Chem Phys (2005) 1.05
The dynamics of proteins. Sci Am (1986) 1.03
Simulation of the diffusion-controlled reaction between superoxide and superoxide dismutase. I. Simple models. Biopolymers (1985) 1.02
Active site binding modes of HIV-1 integrase inhibitors. J Med Chem (2000) 1.02
Theoretical study of hinge bending in L-arabinose-binding protein. Internal energy and free energy changes. J Biol Chem (1983) 1.02
Frictional properties of nonspherical multisubunit structures. Application to tubules and cylinders. Biopolymers (1976) 1.01
Simulation of biomolecular diffusion and complex formation. Biophys J (1986) 1.01
Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories. Protein Sci (1997) 1.01
Intramolecular flexibility in phenylalanine transfer RNA. Nature (1981) 1.00
Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: a molecular dynamics study. J Med Chem (2001) 1.00
Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies. Biophys J (1997) 0.99
Molecular dynamics simulations of the hyperthermophilic protein sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability. J Mol Biol (1999) 0.99
Electrostatic channeling of substrates between enzyme active sites: comparison of simulation and experiment. Biochemistry (1997) 0.98
Simulation methods for protein structure fluctuations. Biopolymers (1980) 0.97
The hinge-bending mode of a lysozyme-inhibitor complex. Biopolymers (1986) 0.97
Molecular properties of amphotericin B membrane channel: a molecular dynamics simulation. Mol Pharmacol (1997) 0.97
Electrostatic effects in homeodomain-DNA interactions. J Mol Biol (1997) 0.96
Large-amplitude bending motions in phenylalanine transfer RNA. Biopolymers (1984) 0.96
Determinants of ligand binding to cAMP-dependent protein kinase. Biochemistry (1999) 0.95
Quantum simulation of ferrocytochrome c. Nature (1988) 0.95
Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase. J Med Chem (1999) 0.94
Molecular dynamics of phenylalanine transfer RNA. J Biomol Struct Dyn (1983) 0.93
Lateral diffusion of membrane proteins in the presence of static and dynamic corrals: suggestions for appropriate observables. Biophys J (2000) 0.93