Published in Proteins on November 01, 2003
Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA (2008) 2.86
Ab initio folding of proteins with all-atom discrete molecular dynamics. Structure (2008) 2.22
In silico study of amyloid beta-protein folding and oligomerization. Proc Natl Acad Sci U S A (2004) 2.13
Multiscale modeling of nucleosome dynamics. Biophys J (2006) 1.63
Molecular dynamics simulation of amyloid beta dimer formation. Biophys J (2004) 1.63
Role of electrostatic interactions in amyloid beta-protein (A beta) oligomer formation: a discrete molecular dynamics study. Biophys J (2007) 1.22
Solvent effects on the conformational transition of a model polyalanine peptide. Protein Sci (2004) 1.20
Generic coarse-grained model for protein folding and aggregation. J Chem Phys (2009) 1.13
Specificity of intramembrane protein-lipid interactions. Cold Spring Harb Perspect Biol (2011) 1.12
Amyloid β-protein oligomers and Alzheimer's disease. Alzheimers Res Ther (2013) 1.07
Side-chain interactions determine amyloid formation by model polyglutamine peptides in molecular dynamics simulations. Biophys J (2006) 1.02
Dimer formation enhances structural differences between amyloid β-protein (1-40) and (1-42): an explicit-solvent molecular dynamics study. PLoS One (2012) 1.01
A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations. J Phys Chem B (2010) 0.98
Structural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase. J Mol Biol (2011) 0.97
Local unfolding of Cu, Zn superoxide dismutase monomer determines the morphology of fibrillar aggregates. J Mol Biol (2011) 0.96
Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model. J Chem Theory Comput (2006) 0.95
Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations. J Mol Graph Model (2010) 0.95
Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations. J Am Chem Soc (2006) 0.94
Monte Carlo studies of folding, dynamics, and stability in alpha-helices. Biophys J (2005) 0.93
Multidimensional persistence in biomolecular data. J Comput Chem (2015) 0.93
Structural basis for Aβ1–42 toxicity inhibition by Aβ C-terminal fragments: discrete molecular dynamics study. J Mol Biol (2011) 0.91
The (1-63) region of the p53 transactivation domain aggregates in vitro into cytotoxic amyloid assemblies. Biophys J (2008) 0.90
Using simple artificial intelligence methods for predicting amyloidogenesis in antibodies. BMC Bioinformatics (2010) 0.90
Phase diagrams describing fibrillization by polyalanine peptides. Biophys J (2004) 0.90
Iron-mediated oxidation induces conformational changes within the redox-sensing protein HbpS. J Biol Chem (2010) 0.88
The toxicity of amyloid β oligomers. Int J Mol Sci (2012) 0.87
Studying the structural properties of polyalanine and polyglutamine peptides. J Mol Model (2007) 0.87
Discrete molecular dynamics study of oligomer formation by N-terminally truncated amyloid β-protein. J Mol Biol (2013) 0.86
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics. Biophys J (2008) 0.86
Probing protein aggregation using discrete molecular dynamics. Front Biosci (2008) 0.86
Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis. Proc Natl Acad Sci U S A (2015) 0.82
Stabilizing Off-pathway Oligomers by Polyphenol Nanoassemblies for IAPP Aggregation Inhibition. Sci Rep (2016) 0.81
α-helix to β-hairpin transition of human amylin monomer. J Chem Phys (2013) 0.80
The mechanism of antiparallel β-sheet formation based on conditioned self-avoiding walk. Eur Phys J E Soft Matter (2012) 0.79
Protein misfolding and aggregation in Alzheimer's disease and type 2 diabetes mellitus. CNS Neurol Disord Drug Targets (2014) 0.79
Inhibition of IAPP aggregation by insulin depends on the insulin oligomeric state regulated by zinc ion concentration. Sci Rep (2015) 0.78
Folding of gas-phase polyalanines in a static electric field: alignment, deformations, and polarization effects. Biophys J (2008) 0.78
Minimal model of self-assembly: emergence of diversity and complexity. J Phys Chem B (2014) 0.78
A free-energy approach for all-atom protein simulation. Biophys J (2009) 0.77
Folding of pig gastric mucin non-glycosylated domains: a discrete molecular dynamics study. J Biol Phys (2012) 0.77
Aggregation of poly(acrylic acid)-containing elastin-mimetic copolymers. Soft Matter (2015) 0.76
Contrasting effects of nanoparticle-protein attraction on amyloid aggregation. RSC Adv (2015) 0.75
Polymorphism of fibrillar structures depending on the size of assembled Aβ17-42 peptides. Sci Rep (2016) 0.75
Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding. PLoS Comput Biol (2015) 0.75
Analysis of the stabilities of hexameric amyloid-β(1-42) models using discrete molecular dynamics simulations. J Mol Graph Model (2010) 0.75
Conformational transitions of the cross-linking domains of elastin during self-assembly. J Biol Chem (2014) 0.75
Aggregation of Chameleon Peptides: Implications of α-Helicity in Fibril Formation. J Phys Chem B (2016) 0.75
Impact of sequence on the molecular assembly of short amyloid peptides. Proteins (2014) 0.75
Recent advances in transferable coarse-grained modeling of proteins. Adv Protein Chem Struct Biol (2014) 0.75
Oxidative stress and the amyloid beta peptide in Alzheimer's disease. Redox Biol (2017) 0.75
Catastrophic cascade of failures in interdependent networks. Nature (2010) 8.35
Fractal dynamics in physiology: alterations with disease and aging. Proc Natl Acad Sci U S A (2002) 7.15
Revisiting Lévy flight search patterns of wandering albatrosses, bumblebees and deer. Nature (2007) 6.94
A theory of power-law distributions in financial market fluctuations. Nature (2003) 5.19
Quantifying trading behavior in financial markets using Google Trends. Sci Rep (2013) 4.84
Complex dynamics of our economic life on different scales: insights from search engine query data. Philos Trans A Math Phys Eng Sci (2010) 4.43
Quantifying the advantage of looking forward. Sci Rep (2012) 4.05
Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function. Proc Natl Acad Sci U S A (2008) 3.08
Switching processes in financial markets. Proc Natl Acad Sci U S A (2011) 2.94
Detrended cross-correlation analysis: a new method for analyzing two nonstationary time series. Phys Rev Lett (2008) 2.86
Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA (2008) 2.86
The growth of business firms: theoretical framework and empirical evidence. Proc Natl Acad Sci U S A (2005) 2.84
Eris: an automated estimator of protein stability. Nat Methods (2007) 2.78
Laws of population growth. Proc Natl Acad Sci U S A (2008) 2.68
Cross-correlations between volume change and price change. Proc Natl Acad Sci U S A (2009) 2.56
Random matrix approach to cross correlations in financial data. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 2.52
Quantitative and empirical demonstration of the Matthew effect in a study of career longevity. Proc Natl Acad Sci U S A (2010) 2.49
Engineered allosteric activation of kinases in living cells. Nat Biotechnol (2010) 2.44
Quantifying the behavior of stock correlations under market stress. Sci Rep (2012) 2.39
Effect of nonstationarities on detrended fluctuation analysis. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 2.35
Emergence of protein fold families through rational design. PLoS Comput Biol (2006) 2.35
Statistical laws governing fluctuations in word use from word birth to word death. Sci Rep (2012) 2.26
Ab initio folding of proteins with all-atom discrete molecular dynamics. Structure (2008) 2.22
Linking agent-based models and stochastic models of financial markets. Proc Natl Acad Sci U S A (2012) 2.20
Common scale-invariant patterns of sleep-wake transitions across mammalian species. Proc Natl Acad Sci U S A (2004) 2.19
Analysis of symbolic sequences using the Jensen-Shannon divergence. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 2.13
Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05
iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics (2008) 2.03
Transport in weighted networks: partition into superhighways and roads. Phys Rev Lett (2006) 1.97
Quantifying stock-price response to demand fluctuations. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 1.95
Transport properties of glass-forming liquids suggest that dynamic crossover temperature is as important as the glass transition temperature. Proc Natl Acad Sci U S A (2010) 1.93
Languages cool as they expand: allometric scaling and the decreasing need for new words. Sci Rep (2012) 1.92
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA (2012) 1.88
Cascading failures in bi-partite graphs: model for systemic risk propagation. Sci Rep (2013) 1.86
Quantifying the digital traces of Hurricane Sandy on Flickr. Sci Rep (2013) 1.85
Elucidating amyloid beta-protein folding and assembly: A multidisciplinary approach. Acc Chem Res (2006) 1.80
Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol (2003) 1.80
Tests of scaling and universality of the distributions of trade size and share volume: evidence from three distinct markets. Phys Rev E Stat Nonlin Soft Matter Phys (2007) 1.80
Dynamic opinion model and invasion percolation. Phys Rev Lett (2009) 1.78
Quantifying fractal dynamics of human respiration: age and gender effects. Ann Biomed Eng (2002) 1.76
Finding a better immunization strategy. Phys Rev Lett (2008) 1.76
Identifying states of a financial market. Sci Rep (2012) 1.76
The competitiveness versus the wealth of a country. Sci Rep (2012) 1.72
Scaling and memory in volatility return intervals in financial markets. Proc Natl Acad Sci U S A (2005) 1.69
Persistence and uncertainty in the academic career. Proc Natl Acad Sci U S A (2012) 1.66
Structure of shells in complex networks. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 1.66
Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J Mol Biol (2002) 1.66
Modeling backbone flexibility improves protein stability estimation. Structure (2007) 1.65
Automated minimization of steric clashes in protein structures. Proteins (2011) 1.64
Multiscale modeling of nucleosome dynamics. Biophys J (2006) 1.63
Non-random fluctuations and multi-scale dynamics regulation of human activity. Physica A (2004) 1.63
Herd behavior in a complex adaptive system. Proc Natl Acad Sci U S A (2011) 1.62
Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating. J Biol Chem (2008) 1.62
On the significance of an RNA tertiary structure prediction. RNA (2010) 1.61
Endogenous circadian rhythm in human motor activity uncoupled from circadian influences on cardiac dynamics. Proc Natl Acad Sci U S A (2007) 1.61
Robustness of a network of networks. Phys Rev Lett (2011) 1.60
Methods for measuring the citations and productivity of scientists across time and discipline. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 1.57
Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J (2002) 1.55
The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54
Computational design of a PAK1 binding protein. J Mol Biol (2010) 1.51
The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis. Proc Natl Acad Sci U S A (2004) 1.46
Modifications of superoxide dismutase (SOD1) in human erythrocytes: a possible role in amyotrophic lateral sclerosis. J Biol Chem (2009) 1.46
Can contact potentials reliably predict stability of proteins? J Mol Biol (2004) 1.44
Robustness of interdependent networks under targeted attack. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 1.44
Bankruptcy risk model and empirical tests. Proc Natl Acad Sci U S A (2010) 1.44
Dynamical robustness of Lévy search strategies. Phys Rev Lett (2003) 1.43
Folding events in the 21-30 region of amyloid beta-protein (Abeta) studied in silico. Proc Natl Acad Sci U S A (2005) 1.43
Statistical regularities in the rank-citation profile of scientists. Sci Rep (2011) 1.40
Simple but predictive protein models. Trends Biotechnol (2005) 1.39
Solvent and mutation effects on the nucleation of amyloid beta-protein folding. Proc Natl Acad Sci U S A (2005) 1.37
MedusaScore: an accurate force field-based scoring function for virtual drug screening. J Chem Inf Model (2008) 1.37
Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J Am Chem Soc (2009) 1.33
Regulatory insertion removal restores maturation, stability and function of DeltaF508 CFTR. J Mol Biol (2010) 1.31
Econophysics: Two-phase behaviour of financial markets. Nature (2003) 1.31
Assortativity decreases the robustness of interdependent networks. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 1.30
Endogenous circadian rhythm in an index of cardiac vulnerability independent of changes in behavior. Proc Natl Acad Sci U S A (2004) 1.30
Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. Biophys J (2004) 1.29
Anomalous transport in scale-free networks. Phys Rev Lett (2005) 1.28
Characterization of sleep stages by correlations in the magnitude and sign of heartbeat increments. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 1.28
Calling patterns in human communication dynamics. Proc Natl Acad Sci U S A (2013) 1.27
Interplay between time-temperature transformation and the liquid-liquid phase transition in water. Phys Rev Lett (2002) 1.26
Asymmetric Lévy flight in financial ratios. Proc Natl Acad Sci U S A (2011) 1.26
Quantifying signals with power-law correlations: a comparative study of detrended fluctuation analysis and detrended moving average techniques. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.26
Fast complementation of split fluorescent protein triggered by DNA hybridization. Proc Natl Acad Sci U S A (2006) 1.26
Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants. Proc Natl Acad Sci U S A (2006) 1.25
Imprint of evolution on protein structures. Proc Natl Acad Sci U S A (2004) 1.24
Spurious detection of phase synchronization in coupled nonlinear oscillators. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 1.23
Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation. Proc Natl Acad Sci U S A (2008) 1.23
Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP. J Am Chem Soc (2010) 1.23
Cascading failures in interdependent lattice networks: the critical role of the length of dependency links. Phys Rev Lett (2012) 1.22
The path of DNA in the kinetochore. Curr Biol (2006) 1.22
Rapid flexible docking using a stochastic rotamer library of ligands. J Chem Inf Model (2010) 1.21
Preferential attachment and growth dynamics in complex systems. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 1.21
Optimal paths in disordered complex networks. Phys Rev Lett (2003) 1.20
Three-dimensional RNA structure refinement by hydroxyl radical probing. Nat Methods (2012) 1.20
Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. J Mol Biol (2005) 1.18
Allosteric modulation balances thermodynamic stability and restores function of ΔF508 CFTR. J Mol Biol (2012) 1.18