Published in J Chem Phys on October 01, 2005
Finding transition pathways using the string method with swarms of trajectories. J Phys Chem B (2008) 2.17
On the assumptions underlying milestoning. J Chem Phys (2008) 1.61
Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin. Proc Natl Acad Sci U S A (2007) 1.50
Milestoning without a Reaction Coordinate. J Chem Theory Comput (2010) 1.47
Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI. J Chem Phys (2011) 1.34
Building Markov state models along pathways to determine free energies and rates of transitions. J Chem Phys (2008) 1.18
Slow conformational motions that favor sub-picosecond motions important for catalysis. J Phys Chem B (2010) 1.13
Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD. Comput Phys Commun (2014) 1.10
Steady-state simulations using weighted ensemble path sampling. J Chem Phys (2010) 1.03
"DFG-flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop. Biophys J (2012) 1.01
Maximum Flux Transition Paths of Conformational Change. J Chem Theory Comput (2010) 0.98
Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin. J Phys Chem B (2012) 0.95
Simulating rare events using a weighted ensemble-based string method. J Chem Phys (2013) 0.94
Calculation of free-energy differences by confinement simulations. Application to peptide conformers. J Phys Chem B (2009) 0.94
Gaussian-mixture umbrella sampling. J Phys Chem B (2009) 0.93
Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible? J Chem Theory Comput (2011) 0.89
String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems. J Chem Theory Comput (2013) 0.85
Energetics and structural characterization of the large-scale functional motion of adenylate kinase. Sci Rep (2015) 0.84
Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems. J Chem Theory Comput (2014) 0.84
Protein dynamics and the enzymatic reaction coordinate. Top Curr Chem (2013) 0.83
Computational delineation of the catalytic step of a high-fidelity DNA polymerase. Protein Sci (2010) 0.83
Recent developments in methods for identifying reaction coordinates. Mol Simul (2014) 0.82
Water pulls the strings in hydrophobic polymer collapse. Proc Natl Acad Sci U S A (2007) 0.80
Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method. J Chem Phys (2014) 0.79
Towards the prediction of order parameters from molecular dynamics simulations in proteins. J Chem Phys (2012) 0.79
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol (2016) 0.78
Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints. J Chem Theory Comput (2012) 0.77
Synthesis and Dynamics of Nanosized Phenylene-Ethynylene-Butadiynylene Rotaxanes and the Role of Shape Persistence. Angew Chem Int Ed Engl (2016) 0.76
Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method. BMC Struct Biol (2013) 0.76
A new perspective on transition states: χ1 separatrix. J Chem Phys (2011) 0.76
Computational delineation of tyrosyl-substrate recognition and catalytic landscapes by the epidermal growth factor receptor tyrosine kinase domain. Mol Biosyst (2014) 0.75
Insight into the molecular mechanism of water evaporation via the finite temperature string method. J Chem Phys (2013) 0.75
Conformational transition paths harbor structures useful for aiding drug discovery and understanding enzymatic mechanisms in protein kinases. Protein Sci (2015) 0.75
Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins (2010) 9.43
Atomic-level characterization of the structural dynamics of proteins. Science (2010) 8.36
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations. Proc Natl Acad Sci U S A (2009) 3.92
Activation mechanism of the β2-adrenergic receptor. Proc Natl Acad Sci U S A (2011) 2.53
String method in collective variables: minimum free energy paths and isocommittor surfaces. J Chem Phys (2006) 2.53
Principles of conduction and hydrophobic gating in K+ channels. Proc Natl Acad Sci U S A (2010) 2.47
Pathway and mechanism of drug binding to G-protein-coupled receptors. Proc Natl Acad Sci U S A (2011) 2.44
Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates. J Chem Phys (2005) 2.37
Systematic validation of protein force fields against experimental data. PLoS One (2012) 2.29
Finite temperature string method for the study of rare events. J Phys Chem B (2005) 2.09
Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics. Proc Natl Acad Sci U S A (2010) 1.97
Transition-path theory and path-finding algorithms for the study of rare events. Annu Rev Phys Chem (2010) 1.95
Simplified and improved string method for computing the minimum energy paths in barrier-crossing events. J Chem Phys (2007) 1.71
Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain. Proc Natl Acad Sci U S A (2007) 1.67
Structure and dynamics of an unfolded protein examined by molecular dynamics simulation. J Am Chem Soc (2012) 1.46
DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator. PLoS One (2010) 1.39
DNA nucleoside interaction and identification with carbon nanotubes. Nano Lett (2007) 1.39
Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI. J Chem Phys (2011) 1.34
Single-sweep methods for free energy calculations. J Chem Phys (2008) 1.32
Illustration of transition path theory on a collection of simple examples. J Chem Phys (2006) 1.31
Markov state models based on milestoning. J Chem Phys (2011) 1.29
Carbon nanotube interaction with DNA. Nano Lett (2005) 1.27
Mapping the network of pathways of CO diffusion in myoglobin. J Am Chem Soc (2010) 1.21
Blue moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics. Chemphyschem (2005) 1.13
Optimal partition and effective dynamics of complex networks. Proc Natl Acad Sci U S A (2008) 1.04
Free energy and kinetics of conformational transitions from Voronoi tessellated milestoning with restraining potentials. J Chem Theory Comput (2009) 0.98
The Inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models. Conf Proc IEEE Eng Med Biol Soc (2009) 0.98
Noise-induced mixed-mode oscillations in a relaxation oscillator near the onset of a limit cycle. Chaos (2008) 0.90
Non-meanfield deterministic limits in chemical reaction kinetics. J Chem Phys (2006) 0.88
Mori-Zwanzig formalism as a practical computational tool. Faraday Discuss (2010) 0.88
Two distinct mechanisms of coherence in randomly perturbed dynamical systems. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.87
Determination of DNA-base orientation on carbon nanotubes through directional optical absorbance. Nano Lett (2007) 0.85
Continuum theory of a moving membrane. Phys Rev E Stat Nonlin Soft Matter Phys (2007) 0.83
Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations. J Am Chem Soc (2015) 0.81
Probabilistic framework for network partition. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.81
Regularity and synchrony in motor proteins. Bull Math Biol (2007) 0.81
Nucleation of ordered phases in block copolymers. Phys Rev Lett (2010) 0.80
Adaptive minimum action method for the study of rare events. J Chem Phys (2008) 0.79
Force-clamp analysis techniques give highest rank to stretched exponential unfolding kinetics in ubiquitin. Biophys J (2012) 0.79
Infinite swapping replica exchange molecular dynamics leads to a simple simulation patch using mixture potentials. J Chem Phys (2013) 0.78
On-the-fly free energy parameterization via temperature accelerated molecular dynamics. Chem Phys Lett (2012) 0.78
Noise can play an organizing role for the recurrent dynamics in excitable media. Proc Natl Acad Sci U S A (2007) 0.77
Kinetic theory for flows of nonhomogeneous rodlike liquid crystalline polymers with a nonlocal intermolecular potential. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 0.76
Regular gaits and optimal velocities for motor proteins. Biophys J (2008) 0.75
Atomistic simulations of rare events using gentlest ascent dynamics. J Chem Phys (2012) 0.75
Pathways of maximum likelihood for rare events in nonequilibrium systems: application to nucleation in the presence of shear. Phys Rev Lett (2008) 0.75
A climbing string method for saddle point search. J Chem Phys (2013) 0.75
New methods: general discussion. Faraday Discuss (2016) 0.75
Modified models of polymer phase separation. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 0.75
A Mathematical Model for Universal Semantics. IEEE Trans Pattern Anal Mach Intell (2022) 0.75