Sub-microsecond protein folding.

The protein folding problem. Annu Rev Biophys (2008) 4.43

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). J Am Chem Soc (2010) 3.18

How robust are protein folding simulations with respect to force field parameterization? Biophys J (2011) 3.00

NMR spectroscopy brings invisible protein states into focus. Nat Chem Biol (2009) 3.00

Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. J Mol Biol (2007) 2.77

Ultrafast dynamics of protein collapse from single-molecule photon statistics. Proc Natl Acad Sci U S A (2007) 2.76

Progress and challenges in the automated construction of Markov state models for full protein systems. J Chem Phys (2009) 2.64

Systematic validation of protein force fields against experimental data. PLoS One (2012) 2.29

Protein folded states are kinetic hubs. Proc Natl Acad Sci U S A (2010) 2.27

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale. J Chem Theory Comput (2011) 2.15

Common structural transitions in explicit-solvent simulations of villin headpiece folding. Biophys J (2009) 1.96

Chemical, physical, and theoretical kinetics of an ultrafast folding protein. Proc Natl Acad Sci U S A (2008) 1.90

Challenges in protein folding simulations: Timescale, representation, and analysis. Nat Phys (2010) 1.67

Force field bias in protein folding simulations. Biophys J (2009) 1.67

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J Chem Theory Comput (2012) 1.65

Atomic-level description of ubiquitin folding. Proc Natl Acad Sci U S A (2013) 1.65

The ribosome modulates nascent protein folding. Science (2011) 1.51

An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain. Proc Natl Acad Sci U S A (2010) 1.47

Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water. Biophys J (2010) 1.47

Protein folding kinetics and thermodynamics from atomistic simulation. Proc Natl Acad Sci U S A (2012) 1.46

Simple few-state models reveal hidden complexity in protein folding. Proc Natl Acad Sci U S A (2012) 1.43

Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding. Proc Natl Acad Sci U S A (2007) 1.42

Distinguishing between cooperative and unimodal downhill protein folding. Proc Natl Acad Sci U S A (2007) 1.35

Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments. J Am Chem Soc (2007) 1.29

Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis. J Am Chem Soc (2009) 1.23

Combining experiment and simulation in protein folding: closing the gap for small model systems. Curr Opin Struct Biol (2008) 1.19

Detection of a transient intermediate in a rapid protein folding process by solid-state nuclear magnetic resonance. J Am Chem Soc (2010) 1.15

Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. J Phys Chem B (2012) 1.14

Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments. Proc Natl Acad Sci U S A (2011) 1.14

Dynamics, energetics, and structure in protein folding. Biochemistry (2006) 1.13

Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates. Proc Natl Acad Sci U S A (2007) 1.06

Quantitative determination of site-specific conformational distributions in an unfolded protein by solid-state nuclear magnetic resonance. J Mol Biol (2009) 1.06

Network models for molecular kinetics and their initial applications to human health. Cell Res (2010) 1.06

Making connections between ultrafast protein folding kinetics and molecular dynamics simulations. Proc Natl Acad Sci U S A (2011) 1.00

X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals. Nat Commun (2014) 0.99

Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles. Protein Sci (2007) 0.99

Modulation of p-cyanophenylalanine fluorescence by amino acid side chains and rational design of fluorescence probes of alpha-helix formation. Biochemistry (2010) 0.92

Induced-fit mechanism for prolyl endopeptidase. J Biol Chem (2010) 0.92

Slow motions in chicken villin headpiece subdomain probed by cross-correlated NMR relaxation of amide NH bonds in successive residues. Biophys J (2008) 0.92

Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations. PLoS One (2012) 0.92

Microsecond folding experiments and simulations: a match is made. Phys Chem Chem Phys (2013) 0.91

Slow motions in the hydrophobic core of chicken villin headpiece subdomain and their contributions to configurational entropy and heat capacity from solid-state deuteron NMR measurements. Biochemistry (2011) 0.91

What can solid state NMR contribute to our understanding of protein folding? Biophys Chem (2010) 0.91

Discrete kinetic models from funneled energy landscape simulations. PLoS One (2012) 0.91

Ultrafast folding kinetics and cooperativity of villin headpiece in single-molecule force spectroscopy. Proc Natl Acad Sci U S A (2013) 0.91

Analysis of the free-energy surface of proteins from reversible folding simulations. PLoS Comput Biol (2009) 0.91

Folding pathways of proteins with increasing degree of sequence identities but different structure and function. Proc Natl Acad Sci U S A (2012) 0.91

Probing the origins of two-state folding. J Chem Phys (2013) 0.90

A simple model predicts experimental folding rates and a hub-like topology. J Phys Chem B (2012) 0.90

Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding. PLoS One (2010) 0.89

The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier. J Chem Phys (2008) 0.89

Reconciling the solution and X-ray structures of the villin headpiece helical subdomain: molecular dynamics simulations and double mutant cycles reveal a stabilizing cation-pi interaction. Biochemistry (2007) 0.89

Conformational dynamics and stability of HP35 studied with 2D IR vibrational echoes. J Am Chem Soc (2012) 0.88

Measuring ultrafast protein folding rates from photon-by-photon analysis of single molecule fluorescence trajectories. Chem Phys (2013) 0.86

Fast protein folding kinetics. Q Rev Biophys (2014) 0.86

The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding. Biophys J (2010) 0.85

Rational modification of protein stability by targeting surface sites leads to complicated results. Proc Natl Acad Sci U S A (2013) 0.84

Importance of contact persistence in denatured state loop formation: kinetic insights into sequence effects on nucleation early in folding. J Mol Biol (2009) 0.83

Glassy dynamics of protein methyl groups revealed by deuteron NMR. J Phys Chem B (2013) 0.83

Investigation of an anomalously accelerating substitution in the folding of a prototypical two-state protein. J Mol Biol (2010) 0.82

The effect of charge-charge interactions on the kinetics of alpha-helix formation. Biophys J (2007) 0.81

Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations. Biophys J (2010) 0.81

Quantitative comparison of alternative methods for coarse-graining biological networks. J Chem Phys (2013) 0.81

Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain. J Biomol NMR (2011) 0.81

Mechanisms of protein folding. Eur Biophys J (2008) 0.80

How to mark off paths on the protein energy landscape. Proc Natl Acad Sci U S A (2009) 0.80

Fast dynamics of HP35 for folded and urea-unfolded conditions. J Phys Chem B (2012) 0.79

Tuning the Attempt Frequency of Protein Folding Dynamics via Transition-State Rigidification: Application to Trp-Cage. J Phys Chem Lett (2015) 0.79

Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data. J Chem Theory Comput (2013) 0.79

Folding of the Pit1 homeodomain near the speed limit. Proc Natl Acad Sci U S A (2010) 0.78

High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant. J Chem Theory Comput (2013) 0.77

Electronic polarization stabilizes tertiary structure prediction of HP-36. J Mol Model (2014) 0.77

Selenomethionine, p-cyanophenylalanine pairs provide a convenient, sensitive, non-perturbing fluorescent probe of local helical structure. Chem Commun (Camb) (2016) 0.77

Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data. Protein Sci (2015) 0.77

Microscopic interpretation of folding ϕ-values using the transition path ensemble. Proc Natl Acad Sci U S A (2016) 0.76

Probing the nanosecond dynamics of a designed three-stranded beta-sheet with a massively parallel molecular dynamics simulation. Int J Mol Sci (2009) 0.76

A compact native 24-residue supersecondary structure derived from the villin headpiece subdomain. Biophys J (2015) 0.76

Dependence of protein crystal stability on residue charge states and ion content of crystal solvent. Biophys J (2014) 0.76

When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches. Biochem J (2016) 0.75

Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions. Int J Mol Sci (2016) 0.75

Effects of Single α-to-β Residue Replacements on Structure and Stability in a Small Protein: Insights from Quasiracemic Crystallization. J Am Chem Soc (2016) 0.75

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model. J Chem Theory Comput (2016) 0.75

Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature (2006) 8.94

Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature (2002) 6.92

The protein folding 'speed limit'. Curr Opin Struct Biol (2004) 6.19

HIF activation identifies early lesions in VHL kidneys: evidence for site-specific tumor suppressor function in the nephron. Cancer Cell (2002) 4.82

Structural basis of toll-like receptor 3 signaling with double-stranded RNA. Science (2008) 4.41

Protein folding studied by single-molecule FRET. Curr Opin Struct Biol (2008) 4.33

Experimental tests of villin subdomain folding simulations. J Mol Biol (2003) 3.08

Single-molecule measurement of protein folding kinetics. Science (2003) 3.08

Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence. Proc Natl Acad Sci U S A (2005) 3.01

Leucine-rich repeats and pathogen recognition in Toll-like receptors. Trends Immunol (2003) 2.82

The molecular structure of the Toll-like receptor 3 ligand-binding domain. Proc Natl Acad Sci U S A (2005) 2.71

Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations. Proc Natl Acad Sci U S A (2007) 2.65

The dsRNA binding site of human Toll-like receptor 3. Proc Natl Acad Sci U S A (2006) 2.37

High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein. Proc Natl Acad Sci U S A (2005) 2.37

Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories. Proc Natl Acad Sci U S A (2009) 2.29

The TLR3 signaling complex forms by cooperative receptor dimerization. Proc Natl Acad Sci U S A (2008) 2.06

The structural biology of Toll-like receptors. Structure (2011) 2.04

Single-molecule fluorescence experiments determine protein folding transition path times. Science (2012) 2.00

Expression of the type 1 insulin-like growth factor receptor is up-regulated in primary prostate cancer and commonly persists in metastatic disease. Cancer Res (2002) 1.98

Chemical, physical, and theoretical kinetics of an ultrafast folding protein. Proc Natl Acad Sci U S A (2008) 1.90

Effect of flexibility and cis residues in single-molecule FRET studies of polyproline. Proc Natl Acad Sci U S A (2007) 1.81

Structure and function of HIV-1 integrase. Curr Top Med Chem (2004) 1.74

Measuring internal friction of an ultrafast-folding protein. Proc Natl Acad Sci U S A (2008) 1.69

Determination of ultrafast protein folding rates from loop formation dynamics. J Mol Biol (2005) 1.42

Effects of denaturants on the dynamics of loop formation in polypeptides. Biophys J (2006) 1.39

Estimating free-energy barrier heights for an ultrafast folding protein from calorimetric and kinetic data. J Phys Chem B (2008) 1.34

Native contacts determine protein folding mechanisms in atomistic simulations. Proc Natl Acad Sci U S A (2013) 1.33

Understanding the shape of sickled red cells. Biophys J (2004) 1.32

Evolution of allosteric models for hemoglobin. IUBMB Life (2007) 1.27

Relaxation rate for an ultrafast folding protein is independent of chemical denaturant concentration. J Am Chem Soc (2007) 1.25

Kinetics of intramolecular contact formation in a denatured protein. J Mol Biol (2003) 1.22

Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopy. Proc Natl Acad Sci U S A (2011) 1.22

Extracting rate coefficients from single-molecule photon trajectories and FRET efficiency histograms for a fast-folding protein. J Phys Chem A (2010) 1.20

A tertiary two-state allosteric model for hemoglobin. Biophys Chem (2002) 1.18

A new crystal structure of deoxyhypusine synthase reveals the configuration of the active enzyme and of an enzyme.NAD.inhibitor ternary complex. J Biol Chem (2004) 1.17

Single-molecule fluorescence probes dynamics of barrier crossing. Nature (2013) 1.15

Distinguishing between protein dynamics and dye photophysics in single-molecule FRET experiments. Biophys J (2010) 1.15

The role of disulfide bonds in the assembly and function of MD-2. Proc Natl Acad Sci U S A (2003) 1.14

Folding and aggregation kinetics of a beta-hairpin. Biochemistry (2006) 1.14

Measuring dynamic flexibility of the coil state of a helix-forming peptide. J Mol Biol (2002) 1.11

New insights into allosteric mechanisms from trapping unstable protein conformations in silica gels. Proc Natl Acad Sci U S A (2004) 1.11

The toll-like receptor 3:dsRNA signaling complex. Biochim Biophys Acta (2009) 1.10

Filaments of the Ure2p prion protein have a cross-beta core structure. J Struct Biol (2005) 1.09

Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scission. Structure (2012) 1.06

Evidence for a partially structured state of the amylin monomer. Biophys J (2009) 1.04

Making connections between ultrafast protein folding kinetics and molecular dynamics simulations. Proc Natl Acad Sci U S A (2011) 1.00

Sedimentation studies on human amylin fail to detect low-molecular-weight oligomers. Biophys J (2008) 1.00

The type 1 insulin-like growth factor receptor is over-expressed in bladder cancer. BJU Int (2007) 0.98

Chemical physics of protein folding. Proc Natl Acad Sci U S A (2012) 0.98

Dimerization of Toll-like receptor 3 (TLR3) is required for ligand binding. J Biol Chem (2010) 0.96

Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations. Proc Natl Acad Sci U S A (2013) 0.94

Solution conformation and dynamics of the HIV-1 integrase core domain. J Biol Chem (2010) 0.94

Induced-fit mechanism for prolyl endopeptidase. J Biol Chem (2010) 0.92

Subclinical rejection and borderline changes in early protocol biopsy specimens after renal transplantation. Transplantation (2004) 0.90

Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry. Acta Crystallogr D Biol Crystallogr (2005) 0.89

Rapidly progressive irreversible renal failure in patients with pancreatic insufficiency. Am J Kidney Dis (2003) 0.89

The molecular structure of the TLR3 extracellular domain. J Endotoxin Res (2006) 0.85

C4d deposition in early renal allograft protocol biopsies. Transplantation (2004) 0.82

Lecithinized superoxide dismutase reduces cold ischemia-induced chronic allograft dysfunction. Kidney Int (2002) 0.79

Re: The relationship between renal tumor size and metastases in patients with von Hippel-Lindau disease. J Urol (2005) 0.75

Tribute to Peter G. Wolynes. J Phys Chem B (2013) 0.75

A tribute to Attila Szabo. J Phys Chem B (2008) 0.75

Young drivers' perceptions of culpability of sleep-deprived versus drinking drivers. J Safety Res (2012) 0.75