Published in Proc Natl Acad Sci U S A on March 30, 2005
Integrated Modeling Program, Applied Chemical Theory (IMPACT). J Comput Chem (2005) 3.71
Protein folded states are kinetic hubs. Proc Natl Acad Sci U S A (2010) 2.27
Reactive flux and folding pathways in network models of coarse-grained protein dynamics. J Chem Phys (2009) 1.93
The AGBNP2 Implicit Solvation Model. J Chem Theory Comput (2009) 1.43
Taming the complexity of protein folding. Curr Opin Struct Biol (2011) 1.35
Understanding ensemble protein folding at atomic detail. Proc Natl Acad Sci U S A (2006) 1.19
Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences. Proteins (2011) 1.16
Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. J Struct Biol (2006) 1.12
Modeling conformational ensembles of slow functional motions in Pin1-WW. PLoS Comput Biol (2010) 1.09
Network models for molecular kinetics and their initial applications to human health. Cell Res (2010) 1.06
Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field. J Mol Biol (2010) 1.04
Microscopic events in β-hairpin folding from alternative unfolded ensembles. Proc Natl Acad Sci U S A (2011) 1.03
Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations. J Am Chem Soc (2011) 1.02
COCIS: Markov processes in single molecule fluorescence. Curr Opin Colloid Interface Sci (2007) 1.02
Simple continuous and discrete models for simulating replica exchange simulations of protein folding. J Phys Chem B (2008) 1.01
How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory. J Phys Chem B (2013) 0.98
Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations. J Phys Chem B (2011) 0.98
Asynchronous replica exchange for molecular simulations. J Comput Chem (2008) 0.97
TIGER2: an improved algorithm for temperature intervals with global exchange of replicas. J Chem Phys (2009) 0.96
Calculation of the free energy and cooperativity of protein folding. PLoS One (2007) 0.96
Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics. J Phys Chem B (2009) 0.96
Building Markov state models with solvent dynamics. BMC Bioinformatics (2013) 0.93
Coarse-grained simulations of protein-protein association: an energy landscape perspective. Biophys J (2012) 0.91
Using Markov state models to study self-assembly. J Chem Phys (2014) 0.89
The temperature intervals with global exchange of replicas empirical accelerated sampling method: parameter sensitivity and extension to a complex molecular system. J Comput Chem (2010) 0.88
The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant. Biophys J (2006) 0.87
Fibril elongation by Aβ(17-42): kinetic network analysis of hybrid-resolution molecular dynamics simulations. J Am Chem Soc (2014) 0.87
NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations. J Phys Chem B (2013) 0.87
Perspective: Markov models for long-timescale biomolecular dynamics. J Chem Phys (2014) 0.85
Graph representation of protein free energy landscape. J Chem Phys (2013) 0.81
Distinguishing among structural ensembles of the GB1 peptide: REMD simulations and NMR experiments. J Am Chem Soc (2007) 0.80
Universality in the timescales of internal loop formation in unfolded proteins and single-stranded oligonucleotides. Biophys J (2010) 0.80
Dual effect of crowders on fibrillation kinetics of polypeptide chains revealed by lattice models. J Chem Phys (2013) 0.79
Predicting the folding pathway of engrailed homeodomain with a probabilistic roadmap enhanced reaction-path algorithm. Biophys J (2007) 0.79
Ensemble-based characterization of unbound and bound states on protein energy landscape. Protein Sci (2013) 0.79
Computational design and experimental discovery of an antiestrogenic peptide derived from alpha-fetoprotein. J Am Chem Soc (2007) 0.79
Identification of folding preferences of cleavage junctions of HIV-1 precursor proteins for regulation of cleavability. J Mol Model (2010) 0.79
A free-energy approach for all-atom protein simulation. Biophys J (2009) 0.77
Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses. Protein Sci (2015) 0.77
Generative models of conformational dynamics. Adv Exp Med Biol (2014) 0.76
Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies. J Chem Theory Comput (2015) 0.76
Inherent structure versus geometric metric for state space discretization. J Comput Chem (2016) 0.75
Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points. J Comput Chem (2016) 0.75
Knowledge-based protein secondary structure assignment. Proteins (1995) 14.08
Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem (1997) 10.65
Folding dynamics and mechanism of beta-hairpin formation. Nature (1997) 7.30
Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem (2001) 7.13
The free energy landscape for beta hairpin folding in explicit water. Proc Natl Acad Sci U S A (2001) 4.39
A short linear peptide that folds into a native stable beta-hairpin in aqueous solution. Nat Struct Biol (1994) 4.17
Fast kinetics and mechanisms in protein folding. Annu Rev Biophys Biomol Struct (2000) 3.90
Exploring the energy landscape of a beta hairpin in explicit solvent. Proteins (2001) 3.88
Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proc Natl Acad Sci U S A (1999) 3.61
Protein folding and unfolding at atomic resolution. Cell (2002) 3.57
AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J Comput Chem (2004) 3.39
Polymer principles and protein folding. Protein Sci (1999) 3.04
Understanding beta-hairpin formation. Proc Natl Acad Sci U S A (1999) 3.01
Cooperativity in protein-folding kinetics. Proc Natl Acad Sci U S A (1993) 2.87
Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. J Mol Biol (2001) 2.78
Understanding protein folding via free-energy surfaces from theory and experiment. Trends Biochem Sci (2000) 2.73
Mechanisms and kinetics of beta-hairpin formation. Proc Natl Acad Sci U S A (2000) 2.66
On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy. J Am Chem Soc (2003) 2.65
The protein folding network. J Mol Biol (2004) 2.63
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers (2003) 2.35
Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. J Chem Phys (2004) 2.30
Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus. J Mol Biol (2000) 2.00
Structural and kinetic characterization of early folding events in beta-lactoglobulin. Nat Struct Biol (2001) 1.97
Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques. Biophys J (1999) 1.68
Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model. Proteins (2004) 1.67
Transition-path sampling of beta-hairpin folding. Proc Natl Acad Sci U S A (2003) 1.61
Identifying the protein folding nucleus using molecular dynamics. J Mol Biol (2000) 1.60
Protein and peptide folding explored with molecular simulations. Acc Chem Res (2002) 1.49
On the simulation of protein folding by short time scale molecular dynamics and distributed computing. Proc Natl Acad Sci U S A (2002) 1.39
Role of side-chains in the cooperative beta-hairpin folding of the short C-terminal fragment derived from streptococcal protein G. Biochemistry (2000) 1.37
Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces. J Mol Biol (2000) 1.36
Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model. Protein Sci (2002) 1.21
Folding of the GB1 hairpin peptide from discrete path sampling. J Chem Phys (2004) 1.17
Evidence of turn and salt bridge contributions to beta-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G. Biophys Chem (2002) 1.12
Complex folding pathways in a simple beta-hairpin. Proteins (2004) 1.09
Kinetic refolding of beta-lactoglobulin. Studies by synchrotron X-ray scattering, and circular dichroism, absorption and fluorescence spectroscopy. J Mol Biol (1998) 1.06
The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions. Biophys Chem (2004) 1.05
Computing the transition state populations in simple protein models. Biopolymers (2003) 0.99
Integrated Modeling Program, Applied Chemical Theory (IMPACT). J Comput Chem (2005) 3.71
AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J Comput Chem (2004) 3.39
On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy. J Am Chem Soc (2003) 2.65
The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. J Comput Chem (2002) 2.52
Temperature weighted histogram analysis method, replica exchange, and transition paths. J Phys Chem B (2005) 2.30
Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models. J Phys Chem A (2003) 1.85
HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site. ACS Chem Biol (2006) 1.83
Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel. Mol Cell (2004) 1.80
Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. J Chem Theory Comput (2008) 1.72
Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model. Proteins (2004) 1.67
Simulating replica exchange simulations of protein folding with a kinetic network model. Proc Natl Acad Sci U S A (2007) 1.65
Biliary cast syndrome following liver transplantation: Predictive factors and clinical outcomes. Liver Transpl (2008) 1.57
The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities. J Chem Theory Comput (2010) 1.52
Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model. Proteins (2002) 1.45
A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Proteins (2007) 1.44
The AGBNP2 Implicit Solvation Model. J Chem Theory Comput (2009) 1.43
Structural reorganization of alpha-synuclein at low pH observed by NMR and REMD simulations. J Mol Biol (2009) 1.39
Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets. J Chem Inf Model (2007) 1.29
Advances in all atom sampling methods for modeling protein-ligand binding affinities. Curr Opin Struct Biol (2011) 1.25
Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein. J Mol Biol (2005) 1.20
Recent theoretical and computational advances for modeling protein-ligand binding affinities. Adv Protein Chem Struct Biol (2011) 1.15
Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. Protein Eng (2003) 1.10
Theory of binless multi-state free energy estimation with applications to protein-ligand binding. J Chem Phys (2012) 1.10
Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). J Comput Aided Mol Des (2012) 1.09
The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions. Biophys Chem (2004) 1.05
Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study. J Am Chem Soc (2006) 1.05
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
Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease. BMC Bioinformatics (2009) 1.02
Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations. J Am Chem Soc (2011) 1.02
Simple continuous and discrete models for simulating replica exchange simulations of protein folding. J Phys Chem B (2008) 1.01
Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. J Chem Theory Comput (2012) 0.99
How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory. J Phys Chem B (2013) 0.98
Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations. J Phys Chem B (2011) 0.98
Asynchronous replica exchange for molecular simulations. J Comput Chem (2008) 0.97
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. J Comput Aided Mol Des (2014) 0.96
Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics. J Phys Chem B (2009) 0.96
Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy. J Theor Biol (2005) 0.95
Identification of alternative binding sites for inhibitors of HIV-1 ribonuclease H through comparative analysis of virtual enrichment studies. J Chem Inf Model (2011) 0.93
Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction. J Struct Funct Genomics (2002) 0.93
In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes. J Mol Biol (2008) 0.91
Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling. Acta Crystallogr D Biol Crystallogr (2008) 0.91
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. J Comput Chem (2010) 0.90
Correlated electrostatic mutations provide a reservoir of stability in HIV protease. PLoS Comput Biol (2012) 0.90
NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations. J Phys Chem B (2013) 0.87
Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes [corrected]. J Mol Biol (2010) 0.85
Conformational dynamics of substrate in the active site of cytochrome P450 BM-3/NPG complex: insights from NMR order parameters. J Am Chem Soc (2007) 0.85
Chimeric rhinoviruses displaying MPER epitopes elicit anti-HIV neutralizing responses. PLoS One (2013) 0.84
Fatal lactic acidosis associated with the use of combination oral medications to treat reactivation of hepatitis B. J Clin Gastroenterol (2009) 0.84
Correlation between 13Calpha chemical shifts and helix content of peptide ensembles. Protein Sci (2008) 0.83
BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. J Comput Aided Mol Des (2015) 0.83
Protein sequential resonance assignments by combinatorial enumeration using 13C alpha chemical shifts and their (i, i-1) sequential connectivities. J Biomol NMR (2002) 0.82
Investigation of the Polymeric Properties of α-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study. J Chem Theory Comput (2012) 0.82
Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease. J Phys Chem B (2014) 0.81
Distinguishing among structural ensembles of the GB1 peptide: REMD simulations and NMR experiments. J Am Chem Soc (2007) 0.80
The linear interaction energy method for the prediction of protein stability changes upon mutation. Proteins (2011) 0.79
Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. J Med Chem (2014) 0.78
Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation. J Chem Theory Comput (2016) 0.78
Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies. J Chem Theory Comput (2015) 0.76
Molecular dynamics of the proline switch and its role in Crk signaling. J Phys Chem B (2014) 0.75
Large-Scale Asynchronous and Distributed Multidimensional Replica Exchange Molecular Simulations and Efficiency Analysis. J Comput Chem (2016) 0.75