Published in J Mol Biol on May 15, 2006
Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins (2006) 22.80
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
Evaluating the performance of the ff99SB force field based on NMR scalar coupling data. Biophys J (2009) 1.61
Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water. Biophys J (2010) 1.47
Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis. J Am Chem Soc (2009) 1.23
Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms. J Mol Biol (2010) 1.23
Using an amino acid fluorescence resonance energy transfer pair to probe protein unfolding: application to the villin headpiece subdomain and the LysM domain. Biochemistry (2008) 1.18
Improved Generalized Born Solvent Model Parameters for Protein Simulations. J Chem Theory Comput (2013) 1.14
Coupling of replica exchange simulations to a non-Boltzmann structure reservoir. J Phys Chem B (2007) 1.12
Uncovering specific electrostatic interactions in the denatured states of proteins. Biophys J (2010) 0.93
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
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
Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain. J Biomol NMR (2011) 0.81
Computational design and experimental discovery of an antiestrogenic peptide derived from alpha-fetoprotein. J Am Chem Soc (2007) 0.79
Thermally induced protein unfolding probed by isotope-edited IR spectroscopy. J Phys Chem B (2012) 0.79
Synergistic applications of MD and NMR for the study of biological systems. J Biomed Biotechnol (2012) 0.79
Isoform-specific interactions of the von Hippel-Lindau tumor suppressor protein. Sci Rep (2015) 0.77
Electronic polarization stabilizes tertiary structure prediction of HP-36. J Mol Model (2014) 0.77
A compact native 24-residue supersecondary structure derived from the villin headpiece subdomain. Biophys J (2015) 0.76
Nascent β-Hairpin Formation of a Natively Unfolded Peptide Reveals the Role of Hydrophobic Contacts. Biophys J (2015) 0.76
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The free energy landscape for beta hairpin folding in explicit water. Proc Natl Acad Sci U S A (2001) 4.39
Exploring the energy landscape of a beta hairpin in explicit solvent. Proteins (2001) 3.88
Polyproline II structure in a sequence of seven alanine residues. Proc Natl Acad Sci U S A (2002) 3.54
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Persistence of native-like topology in a denatured protein in 8 M urea. Science (2001) 3.38
Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins. Proc Natl Acad Sci U S A (2003) 3.34
HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proc Natl Acad Sci U S A (2006) 3.30
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Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. J Comput Chem (2003) 2.49
Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins (2003) 2.39
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
Solution structure of a protein denatured state and folding intermediate. Nature (2005) 2.33
Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent. Proc Natl Acad Sci U S A (2003) 2.31
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Free-energy landscape of the villin headpiece in an all-atom force field. Structure (2005) 1.89
Peptide models provide evidence for significant structure in the denatured state of a rapidly folding protein: the villin headpiece subdomain. Biochemistry (2004) 1.89
Ab initio folding of helix bundle proteins using molecular dynamics simulations. J Am Chem Soc (2003) 1.86
Probing site-specific conformational distributions in protein folding with solid-state NMR. Proc Natl Acad Sci U S A (2005) 1.57
The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain. Protein Sci (2002) 1.56
Application of the diffusion-collision model to the folding of three-helix bundle proteins. J Mol Biol (2002) 1.53
All-atom generalized-ensemble simulations of small proteins. J Mol Graph Model (2004) 1.52
The denatured state of Engrailed Homeodomain under denaturing and native conditions. J Mol Biol (2003) 1.51
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Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment. J Mol Biol (2004) 1.46
Circular dichroism spectra of short, fixed-nucleus alanine helices. Proc Natl Acad Sci U S A (2002) 1.42
Assessing equilibration and convergence in biomolecular simulations. Proteins (2002) 1.40
UV Raman demonstrates that alpha-helical polyalanine peptides melt to polyproline II conformations. J Am Chem Soc (2004) 1.36
Theoretical CD studies of polypeptide helices: examination of important electronic and geometric factors. Biopolymers (1991) 1.33
Unfolded state of polyalanine is a segmented polyproline II helix. Proteins (2004) 1.25
Helix-coil transition of alanine peptides in water: force field dependence on the folded and unfolded structures. Proteins (2005) 1.23
Mutational analysis demonstrates that specific electrostatic interactions can play a key role in the denatured state ensemble of proteins. J Mol Biol (2005) 1.21
Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics. Proteins (2005) 1.18
Alpha-helix nucleation by a calcium-binding peptide loop. Proc Natl Acad Sci U S A (1999) 1.18
Folding cooperativity in a three-stranded beta-sheet model. J Mol Biol (2005) 1.15
Investigation of Salt Bridge Stability in a Generalized Born Solvent Model. J Chem Theory Comput (2006) 1.12
Role of backbone hydration and salt-bridge formation in stability of alpha-helix in solution. Biophys J (2003) 1.10
Conformation spaces of proteins. Proteins (2001) 1.09
Comparative study of generalized Born models: protein dynamics. Proc Natl Acad Sci U S A (2005) 1.08
Large-scale context in protein folding: villin headpiece. Biochemistry (2003) 1.07
Solution structures of the C-terminal headpiece subdomains of human villin and advillin, evaluation of headpiece F-actin-binding requirements. Protein Sci (2004) 1.05
Conformational sampling for the impatient. Biophys Chem (2004) 1.02
Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins (2006) 22.80
HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proc Natl Acad Sci U S A (2006) 3.30
Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. J Comput Chem (2003) 2.49
Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction. Nat Chem Biol (2011) 2.39
Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation. Nat Struct Mol Biol (2009) 2.32
Two-dimensional IR spectroscopy and isotope labeling defines the pathway of amyloid formation with residue-specific resolution. Proc Natl Acad Sci U S A (2009) 2.02
Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci (2005) 1.91
Peptide models provide evidence for significant structure in the denatured state of a rapidly folding protein: the villin headpiece subdomain. Biochemistry (2004) 1.89
Dynamic NMR line-shape analysis demonstrates that the villin headpiece subdomain folds on the microsecond time scale. J Am Chem Soc (2003) 1.82
Location of Trp265 in metarhodopsin II: implications for the activation mechanism of the visual receptor rhodopsin. J Mol Biol (2006) 1.69
The flavanol (-)-epigallocatechin 3-gallate inhibits amyloid formation by islet amyloid polypeptide, disaggregates amyloid fibrils, and protects cultured cells against IAPP-induced toxicity. Biochemistry (2010) 1.63
Evaluating the performance of the ff99SB force field based on NMR scalar coupling data. Biophys J (2009) 1.61
A single-point mutation converts the highly amyloidogenic human islet amyloid polypeptide into a potent fibrillization inhibitor. J Am Chem Soc (2007) 1.59
Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain. Proc Natl Acad Sci U S A (2005) 1.55
Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal. J Mol Biol (2002) 1.51
Residue specific resolution of protein folding dynamics using isotope-edited infrared temperature jump spectroscopy. Biochemistry (2007) 1.51
A role for helical intermediates in amyloid formation by natively unfolded polypeptides? Phys Biol (2009) 1.49
HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state. J Am Chem Soc (2006) 1.49
Location of the retinal chromophore in the activated state of rhodopsin*. J Biol Chem (2009) 1.48
Characterizing a partially folded intermediate of the villin headpiece domain under non-denaturing conditions: contribution of His41 to the pH-dependent stability of the N-terminal subdomain. J Mol Biol (2005) 1.47
The role of His-18 in amyloid formation by human islet amyloid polypeptide. Biochemistry (2005) 1.46
Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation. J Phys Chem B (2007) 1.43
Two-dimensional infrared spectroscopy reveals the complex behaviour of an amyloid fibril inhibitor. Nat Chem (2012) 1.39
Modified replica exchange simulation methods for local structure refinement. J Phys Chem B (2005) 1.39
A critical assessment of the role of helical intermediates in amyloid formation by natively unfolded proteins and polypeptides. Protein Eng Des Sel (2009) 1.38
Multistate folding of the villin headpiece domain. J Mol Biol (2005) 1.36
Recovery and purification of highly aggregation-prone disulfide-containing peptides: application to islet amyloid polypeptide. Anal Biochem (2005) 1.36
Rifampicin does not prevent amyloid fibril formation by human islet amyloid polypeptide but does inhibit fibril thioflavin-T interactions: implications for mechanistic studies of beta-cell death. Biochemistry (2008) 1.32
Incorporation of pseudoproline derivatives allows the facile synthesis of human IAPP, a highly amyloidogenic and aggregation-prone polypeptide. Org Lett (2005) 1.29
Temperature-dependent dynamics of the villin headpiece helical subdomain, an unusually small thermostable protein. J Mol Biol (2002) 1.28
Interpretation of p-cyanophenylalanine fluorescence in proteins in terms of solvent exposure and contribution of side-chain quenchers: a combined fluorescence, IR and molecular dynamics study. Biochemistry (2009) 1.25
Use of the tubulin bound paclitaxel conformation for structure-based rational drug design. Chem Biol (2005) 1.24
Aromatic interactions are not required for amyloid fibril formation by islet amyloid polypeptide but do influence the rate of fibril formation and fibril morphology. Biochemistry (2007) 1.24
The ability of rodent islet amyloid polypeptide to inhibit amyloid formation by human islet amyloid polypeptide has important implications for the mechanism of amyloid formation and the design of inhibitors. Biochemistry (2010) 1.21
Mutational analysis demonstrates that specific electrostatic interactions can play a key role in the denatured state ensemble of proteins. J Mol Biol (2005) 1.21
Low levels of asparagine deamidation can have a dramatic effect on aggregation of amyloidogenic peptides: implications for the study of amyloid formation. Protein Sci (2002) 1.20
Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient β-sheet. Proc Natl Acad Sci U S A (2013) 1.20
2DIR spectroscopy of human amylin fibrils reflects stable β-sheet structure. J Am Chem Soc (2011) 1.20
Destabilization of human IAPP amyloid fibrils by proline mutations outside of the putative amyloidogenic domain: is there a critical amyloidogenic domain in human IAPP? J Mol Biol (2005) 1.19
Azidohomoalanine: a conformationally sensitive IR probe of protein folding, protein structure, and electrostatics. Angew Chem Int Ed Engl (2010) 1.17
Rapid cooperative two-state folding of a miniature alpha-beta protein and design of a thermostable variant. J Mol Biol (2003) 1.17
Strategies for extracting structural information from 2D IR spectroscopy of amyloid: application to islet amyloid polypeptide. J Phys Chem B (2009) 1.16
Folding cooperativity in a three-stranded beta-sheet model. J Mol Biol (2005) 1.15
Role of aromatic interactions in amyloid formation by peptides derived from human Amylin. Biochemistry (2004) 1.14
Analysis of the inhibition and remodeling of islet amyloid polypeptide amyloid fibers by flavanols. Biochemistry (2012) 1.13
Structure of a transient intermediate for GTP hydrolysis by ras. Structure (2006) 1.13
Efficient microwave-assisted synthesis of human islet amyloid polypeptide designed to facilitate the specific incorporation of labeled amino acids. Org Lett (2010) 1.13
Thio-glucose bound gold nanoparticles enhance radio-cytotoxic targeting of ovarian cancer. Nanotechnology (2011) 1.12
Coupling of replica exchange simulations to a non-Boltzmann structure reservoir. J Phys Chem B (2007) 1.12
Fine structure analysis of a protein folding transition state; distinguishing between hydrophobic stabilization and specific packing. J Mol Biol (2005) 1.12
Denatured state effects and the origin of nonclassical phi values in protein folding. J Am Chem Soc (2006) 1.10
Dynamic behavior of DNA base pairs containing 8-oxoguanine. J Am Chem Soc (2005) 1.09
Islet amyloid: from fundamental biophysics to mechanisms of cytotoxicity. FEBS Lett (2013) 1.08
Temporal variations of surface water quality in urban, suburban and rural areas during rapid urbanization in Shanghai, China. Environ Pollut (2007) 1.08
Two-dimensional infrared spectroscopy provides evidence of an intermediate in the membrane-catalyzed assembly of diabetic amyloid. J Phys Chem B (2009) 1.07
Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network. J Am Chem Soc (2007) 1.07
Islet amyloid polypeptide toxicity and membrane interactions. Proc Natl Acad Sci U S A (2013) 1.06
Ion mobility spectrometry-mass spectrometry defines the oligomeric intermediates in amylin amyloid formation and the mode of action of inhibitors. J Am Chem Soc (2013) 1.06
Exploiting the right side of the Ramachandran plot: substitution of glycines by D-alanine can significantly increase protein stability. J Am Chem Soc (2004) 1.05
Comparison of class A and D G protein-coupled receptors: common features in structure and activation. Biochemistry (2005) 1.05
Morin hydrate inhibits amyloid formation by islet amyloid polypeptide and disaggregates amyloid fibers. Protein Sci (2012) 1.05
Combination of kinetically selected inhibitors in trans leads to highly effective inhibition of amyloid formation. J Am Chem Soc (2010) 1.04
Aggregation of islet amyloid polypeptide: from physical chemistry to cell biology. Curr Opin Struct Biol (2012) 1.04
Characterizing septum inhibition in Mycobacterium tuberculosis for novel drug discovery. Tuberculosis (Edinb) (2008) 1.04
The open structure of a multi-drug-resistant HIV-1 protease is stabilized by crystal packing contacts. J Am Chem Soc (2006) 1.04
The fluorescent amino acid p-cyanophenylalanine provides an intrinsic probe of amyloid formation. Chembiochem (2008) 1.03
Amyloid formation by pro-islet amyloid polypeptide processing intermediates: examination of the role of protein heparan sulfate interactions and implications for islet amyloid formation in type 2 diabetes. Biochemistry (2007) 1.03
Deamidation accelerates amyloid formation and alters amylin fiber structure. J Am Chem Soc (2012) 1.03
Role of group-conserved residues in the helical core of beta2-adrenergic receptor. Proc Natl Acad Sci U S A (2007) 1.02
Electrostatic interactions in the denatured state ensemble: their effect upon protein folding and protein stability. Arch Biochem Biophys (2007) 1.01
NMR characterization of a peptide model provides evidence for significant structure in the unfolded state of the villin headpiece helical subdomain. Biochemistry (2006) 1.01
Solution structure and folding characteristics of the C-terminal SH3 domain of c-Crk-II. Biochemistry (2006) 1.00
Comparison of random forest and Pipeline Pilot Naïve Bayes in prospective QSAR predictions. J Chem Inf Model (2012) 1.00
The sulfated triphenyl methane derivative acid fuchsin is a potent inhibitor of amyloid formation by human islet amyloid polypeptide and protects against the toxic effects of amyloid formation. J Mol Biol (2010) 1.00
Sensitivity of amyloid formation by human islet amyloid polypeptide to mutations at residue 20. J Mol Biol (2011) 1.00
Rational design, structural and thermodynamic characterization of a hyperstable variant of the villin headpiece helical subdomain. Biochemistry (2007) 0.99
Ionic strength effects on amyloid formation by amylin are a complicated interplay among Debye screening, ion selectivity, and Hofmeister effects. Biochemistry (2012) 0.99
Electrostatic interactions in the denatured state and in the transition state for protein folding: effects of denatured state interactions on the analysis of transition state structure. J Mol Biol (2006) 0.98
Native like structure in the unfolded state of the villin headpiece helical subdomain, an ultrafast folding protein. Protein Sci (2009) 0.98
A simple and economical method for the production of 13C,18O-labeled Fmoc-amino acids with high levels of enrichment: applications to isotope-edited IR studies of proteins. Org Lett (2007) 0.98
Differential ordering of the protein backbone and side chains during protein folding revealed by site-specific recombinant infrared probes. J Am Chem Soc (2011) 0.97
Insight through molecular mechanics Poisson-Boltzmann surface area calculations into the binding affinity of triclosan and three analogues for FabI, the E. coli enoyl reductase. J Med Chem (2006) 0.97
Computational analysis of the mode of binding of 8-oxoguanine to formamidopyrimidine-DNA glycosylase. Biochemistry (2006) 0.97
Neprilysin impedes islet amyloid formation by inhibition of fibril formation rather than peptide degradation. J Biol Chem (2010) 0.96
Experiments and simulations show how long-range contacts can form in expanded unfolded proteins with negligible secondary structure. Proc Natl Acad Sci U S A (2013) 0.96
Characterization of large peptide fragments derived from the N-terminal domain of the ribosomal protein L9: definition of the minimum folding motif and characterization of local electrostatic interactions. Biochemistry (2002) 0.95
Beyond the decoupling approximation in the model free approach for the interpretation of NMR relaxation of macromolecules in solution. J Am Chem Soc (2003) 0.95
Contribution to stability and folding of a buried polar residue at the CARM1 methylation site of the KIX domain of CBP. Biochemistry (2003) 0.94
Rational design of potent domain antibody inhibitors of amyloid fibril assembly. Proc Natl Acad Sci U S A (2012) 0.94
The unfolded state of the C-terminal domain of the ribosomal protein L9 contains both native and non-native structure. Biochemistry (2009) 0.93
Role of aromatic interactions in amyloid formation by islet amyloid polypeptide. Biochemistry (2013) 0.93
pH-dependent stability and folding kinetics of a protein with an unusual alpha-beta topology: the C-terminal domain of the ribosomal protein L9. J Mol Biol (2002) 0.93
Direct characterization of the folded, unfolded and urea-denatured states of the C-terminal domain of the ribosomal protein L9. J Mol Biol (2005) 0.93
Modulation of p-cyanophenylalanine fluorescence by amino acid side chains and rational design of fluorescence probes of alpha-helix formation. Biochemistry (2010) 0.92
Analysis of core packing in a cooperatively folded miniature protein: the ultrafast folding villin headpiece helical subdomain. Biochemistry (2009) 0.92