Published in J Am Chem Soc on February 23, 2015
Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. PLoS Comput Biol (2015) 0.81
Effect of Outer-Sphere Side Chain Substitutions on the Fate of the trans Iron-Nitrosyl Dimer in Heme/Nonheme Engineered Myoglobins (FeBMbs): Insights into the Mechanism of Denitrifying NO Reductases. Biochemistry (2016) 0.76
Multiscale implementation of infinite-swap replica exchange molecular dynamics. Proc Natl Acad Sci U S A (2016) 0.75
SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding. J Phys Chem B (2017) 0.75
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations. Proc Natl Acad Sci U S A (2009) 3.92
String method in collective variables: minimum free energy paths and isocommittor surfaces. J Chem Phys (2006) 2.53
Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates. J Chem Phys (2005) 2.37
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
Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide. J Chem Phys (2005) 1.63
The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities. J Chem Theory Comput (2010) 1.52
DREAM3: network inference using dynamic context likelihood of relatedness and the inferelator. PLoS One (2010) 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
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
Theory of binless multi-state free energy estimation with applications to protein-ligand binding. J Chem Phys (2012) 1.10
Optimal partition and effective dynamics of complex networks. Proc Natl Acad Sci U S A (2008) 1.04
"DFG-flip" in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop. Biophys J (2012) 1.01
The Inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models. Conf Proc IEEE Eng Med Biol Soc (2009) 0.98
Free energy and kinetics of conformational transitions from Voronoi tessellated milestoning with restraining potentials. J Chem Theory Comput (2009) 0.98
A computational study of water and CO migration sites and channels inside myoglobin. J Chem Theory Comput (2013) 0.95
A model of peptide triazole entry inhibitor binding to HIV-1 gp120 and the mechanism of bridging sheet disruption. Biochemistry (2013) 0.90
All-atom models of the membrane-spanning domain of HIV-1 gp41 from metadynamics. Biophys J (2010) 0.90
Noise-induced mixed-mode oscillations in a relaxation oscillator near the onset of a limit cycle. Chaos (2008) 0.90
Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex. Biophys J (2008) 0.89
Strategies to enhance capillary formation inside biomaterials: a computational study. Tissue Eng (2007) 0.89
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
All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element. Proteins (2013) 0.84
Chimeric rhinoviruses displaying MPER epitopes elicit anti-HIV neutralizing responses. PLoS One (2013) 0.84
All-atom structural models for complexes of insulin-like growth factors IGF1 and IGF2 with their cognate receptor. J Mol Biol (2010) 0.84
Spontaneous conformational changes in the E. coli GroEL subunit from all-atom molecular dynamics simulations. Biophys J (2007) 0.84
Mapping spatial relationships between residues in the ligand-binding domain of the 5-HT3 receptor using a molecular ruler. Biophys J (2010) 0.82
Regularity and synchrony in motor proteins. Bull Math Biol (2007) 0.81
Arrested swelling of highly entangled polymer globules. Phys Rev Lett (2003) 0.80
Chemotaxis and random motility in unsteady chemoattractant fields: a computational study. J Theor Biol (2005) 0.79
Energetics and mechanism of the normal-to-amyloidogenic isomerization of β2-microglobulin: on-the-fly string method calculations. J Phys Chem B (2012) 0.79
Docking of insulin to a structurally equilibrated insulin receptor ectodomain. Proteins (2010) 0.79
Force-clamp analysis techniques give highest rank to stretched exponential unfolding kinetics in ubiquitin. Biophys J (2012) 0.79
Enhanced meta-analysis of acetylcholine binding protein structures reveals conformational signatures of agonism in nicotinic receptors. Protein Sci (2012) 0.79
Dynamics of lipids, cholesterol, and transmembrane α-helices from microsecond molecular dynamics simulations. J Phys Chem B (2014) 0.78
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
Computational Evaluation of HIV-1 gp120 Conformations of Soluble Trimeric gp140 Structures as Targets for de Novo Docking of First- and Second-Generation Small-Molecule CD4 Mimics. J Chem Inf Model (2016) 0.77
Simulations of chemotaxis and random motility in 2D random porous domains. Bull Math Biol (2007) 0.77
Noise can play an organizing role for the recurrent dynamics in excitable media. Proc Natl Acad Sci U S A (2007) 0.77
A mechanism by which binding of the broadly neutralizing antibody b12 unfolds the inner domain α1 helix in an engineered HIV-1 gp120. Proteins (2011) 0.77
Regular gaits and optimal velocities for motor proteins. Biophys J (2008) 0.75
Transition-Path Theory Calculations on Non-Uniform Meshes in Two and Three Dimensions using Finite Elements. Comput Phys Commun (2013) 0.75
Covalent conjugation of a peptide triazole to HIV-1 gp120 enables intramolecular binding site occupancy. Biochemistry (2014) 0.75
A climbing string method for saddle point search. J Chem Phys (2013) 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
Microvoid formation and strain hardening in highly cross-linked polymer networks. Phys Rev E Stat Nonlin Soft Matter Phys (2008) 0.75
New methods: general discussion. Faraday Discuss (2016) 0.75
Kinetics of a polysoap collapse. J Chem Phys (2004) 0.75
Kinetics of O2 Entry and Exit in Monomeric Sarcosine Oxidase via Markovian Milestoning Molecular Dynamics. J Chem Theory Comput (2016) 0.75
Anomalous ductility in thermoset/thermoplastic polymer alloys. Phys Chem Chem Phys (2009) 0.75
Mechanical behavior of highly cross-linked polymer networks and its links to microscopic structure. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.75