Published in Biophys J on April 11, 2008
Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science (2003) 18.18
A structural model for Alzheimer's beta -amyloid fibrils based on experimental constraints from solid state NMR. Proc Natl Acad Sci U S A (2002) 9.55
3D structure of Alzheimer's amyloid-beta(1-42) fibrils. Proc Natl Acad Sci U S A (2005) 8.60
Correlation of structural elements and infectivity of the HET-s prion. Nature (2005) 4.01
Amyloid formation under physiological conditions proceeds via a native-like folding intermediate. Nat Struct Mol Biol (2006) 2.82
The prolyl isomerase Pin1 regulates amyloid precursor protein processing and amyloid-beta production. Nature (2006) 2.61
On the nucleation of amyloid beta-protein monomer folding. Protein Sci (2005) 2.47
Are amyloid diseases caused by protein aggregates that mimic bacterial pore-forming toxins? Q Rev Biophys (2006) 2.47
The Alzheimer's peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study. J Mol Biol (2007) 2.35
The Alzheimer's peptide a beta adopts a collapsed coil structure in water. J Struct Biol (2000) 2.26
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations. Proc Natl Acad Sci U S A (2006) 2.23
Abeta40-Lactam(D23/K28) models a conformation highly favorable for nucleation of amyloid. Biochemistry (2005) 1.78
General structural motifs of amyloid protofilaments. Proc Natl Acad Sci U S A (2006) 1.72
Conformation-dependent anti-amyloid oligomer antibodies. Methods Enzymol (2006) 1.72
3D structure of amyloid protofilaments of beta2-microglobulin fragment probed by solid-state NMR. Proc Natl Acad Sci U S A (2006) 1.70
Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains. J Am Chem Soc (2005) 1.60
The solution structure of human beta2-microglobulin reveals the prodromes of its amyloid transition. Protein Sci (2002) 1.44
Amyloid fibril formation in the context of full-length protein: effects of proline mutations on the amyloid fibril formation of beta2-microglobulin. J Biol Chem (2003) 1.31
Investigation of a peptide responsible for amyloid fibril formation of beta 2-microglobulin by achromobacter protease I. J Biol Chem (2001) 1.27
Locally disordered conformer of the hamster prion protein: a crucial intermediate to PrPSc? Biochemistry (2002) 1.24
Essential role of proline isomerization in stefin B tetramer formation. J Mol Biol (2006) 1.23
Seeding-dependent propagation and maturation of amyloid fibril conformation. J Mol Biol (2005) 1.15
A strand-loop-strand structure is a possible intermediate in fibril elongation: long time simulations of amyloid-beta peptide (10-35). J Am Chem Soc (2005) 1.07
Secondary structure determines protein topology. Protein Sci (2006) 1.00
Structural and hydration properties of the partially unfolded states of the prion protein. Biophys J (2007) 0.99
Properties of some variants of human beta2-microglobulin and amyloidogenesis. J Biol Chem (2003) 0.98
Folding of the yeast prion protein Ure2: kinetic evidence for folding and unfolding intermediates. J Mol Biol (2002) 0.88
A cylinder-shaped double ribbon structure formed by an amyloid hairpin peptide derived from the beta-sheet of murine PrP: an X-ray and molecular dynamics simulation study. J Struct Biol (2005) 0.81
Structure and aggregation mechanism of beta(2)-microglobulin (83-99) peptides studied by molecular dynamics simulations. Biophys J (2007) 0.78
PEP-FOLD: an online resource for de novo peptide structure prediction. Nucleic Acids Res (2009) 1.87
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Res (2012) 1.71
Structural Modelling of the Sm-like Protein Hfq from Escherichia coli. J Mol Biol (2002) 1.29
The C-terminal domain of Escherichia coli Hfq increases the stability of the hexamer. Eur J Biochem (2004) 1.25
A coarse-grained protein force field for folding and structure prediction. Proteins (2007) 1.21
A fast method for large-scale de novo peptide and miniprotein structure prediction. J Comput Chem (2010) 1.20
Plugging into proteins: poisoning protein function by a hydrophobic nanoparticle. ACS Nano (2010) 1.17
Pathway complexity of Alzheimer's beta-amyloid Abeta16-22 peptide assembly. Structure (2004) 1.14
Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev (2015) 1.10
Role of the region 23-28 in Abeta fibril formation: insights from simulations of the monomers and dimers of Alzheimer's peptides Abeta40 and Abeta42. Curr Alzheimer Res (2008) 1.09
Complex folding pathways in a simple beta-hairpin. Proteins (2004) 1.09
The conformations of the amyloid-beta (21-30) fragment can be described by three families in solution. J Chem Phys (2006) 1.07
Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent. Proteins (2009) 1.03
In silico assembly of Alzheimer's Abeta16-22 peptide into beta-sheets. J Am Chem Soc (2004) 1.02
Structures and thermodynamics of Alzheimer's amyloid-beta Abeta(16-35) monomer and dimer by replica exchange molecular dynamics simulations: implication for full-length Abeta fibrillation. J Phys Chem B (2009) 1.01
Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent. J Phys Chem B (2009) 1.01
Structural and hydration properties of the partially unfolded states of the prion protein. Biophys J (2007) 0.99
Coarse-grained protein molecular dynamics simulations. J Chem Phys (2007) 0.98
Targeting the early steps of Abeta16-22 protofibril disassembly by N-methylated inhibitors: a numerical study. Proteins (2009) 0.97
Improved greedy algorithm for protein structure reconstruction. J Comput Chem (2005) 0.97
Hfq variant with altered RNA binding functions. Nucleic Acids Res (2006) 0.96
Impact of the mutation A21G (Flemish variant) on Alzheimer's beta-amyloid dimers by molecular dynamics simulations. Biophys J (2006) 0.96
Structures of soluble amyloid oligomers from computer simulations. Proteins (2006) 0.95
Distinct dimerization for various alloforms of the amyloid-beta protein: Aβ(1-40), Aβ(1-42), and Aβ(1-40)(D23N). J Phys Chem B (2012) 0.95
Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ(16-22) dimer and trimer. Phys Chem Chem Phys (2011) 0.93
Sampling the self-assembly pathways of KFFE hexamers. Biophys J (2004) 0.93
Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm. Proteins (2005) 0.93
Exploring the early steps of amyloid peptide aggregation by computers. Acc Chem Res (2005) 0.93
Interactions of Aβ25-35 β-barrel-like oligomers with anionic lipid bilayer and resulting membrane leakage: an all-atom molecular dynamics study. J Phys Chem B (2010) 0.92
Computational simulations of the early steps of protein aggregation. Prion (2007) 0.92
HiRE-RNA: a high resolution coarse-grained energy model for RNA. J Phys Chem B (2010) 0.92
Structural diversity of the soluble trimers of the human amylin(20-29) peptide revealed by molecular dynamics simulations. J Chem Phys (2009) 0.91
Self-assembly of the beta2-microglobulin NHVTLSQ peptide using a coarse-grained protein model reveals a beta-barrel species. J Phys Chem B (2008) 0.91
Conformational basis for asymmetric seeding barrier in filaments of three- and four-repeat tau. J Am Chem Soc (2012) 0.91
Structures of Aβ17-42 trimers in isolation and with five small-molecule drugs using a hierarchical computational procedure. J Phys Chem B (2012) 0.91
A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35. PLoS Comput Biol (2011) 0.89
Effect of the disulfide bond on the monomeric structure of human amylin studied by combined Hamiltonian and temperature replica exchange molecular dynamics simulations. J Phys Chem B (2010) 0.89
Probing the self-assembly mechanism of diphenylalanine-based peptide nanovesicles and nanotubes. ACS Nano (2012) 0.88
The coarse-grained OPEP force field for non-amyloid and amyloid proteins. J Phys Chem B (2012) 0.88
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev (2014) 0.88
Effect of the Tottori familial disease mutation (D7N) on the monomers and dimers of Aβ40 and Aβ42. ACS Chem Neurosci (2013) 0.88
Atomic-level study of adsorption, conformational change, and dimerization of an α-helical peptide at graphene surface. J Phys Chem B (2011) 0.88
Low molecular weight oligomers of amyloid peptides display beta-barrel conformations: a replica exchange molecular dynamics study in explicit solvent. J Chem Phys (2010) 0.87
Familial Alzheimer A2 V mutation reduces the intrinsic disorder and completely changes the free energy landscape of the Aβ1-28 monomer. J Phys Chem B (2014) 0.87
Molecular mechanism of the inhibition of EGCG on the Alzheimer Aβ(1-42) dimer. J Phys Chem B (2013) 0.87
Structure and thermodynamics of amylin dimer studied by Hamiltonian-temperature replica exchange molecular dynamics simulations. J Phys Chem B (2011) 0.87
The antitumor properties of the alpha3(IV)-(185-203) peptide from the NC1 domain of type IV collagen (tumstatin) are conformation-dependent. J Biol Chem (2003) 0.87
Cross-seeding and conformational selection between three- and four-repeat human Tau proteins. J Biol Chem (2012) 0.87
Probing amyloid fibril formation of the NFGAIL peptide by computer simulations. J Chem Phys (2007) 0.86
Molecular dynamics simulations of the bacterial ABC transporter SAV1866 in the closed form. J Phys Chem B (2012) 0.86
Aggregating the amyloid Abeta(11-25) peptide into a four-stranded beta-sheet structure. Proteins (2006) 0.86
Probing ion channel activity of human islet amyloid polypeptide (amylin). Biochim Biophys Acta (2012) 0.86
Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches. J R Soc Interface (2011) 0.86
Impact of the tail and mutations G131V and M129V on prion protein flexibility. Proteins (2003) 0.86
Lipid interaction and membrane perturbation of human islet amyloid polypeptide monomer and dimer by molecular dynamics simulations. PLoS One (2012) 0.85
Carbon nanotube inhibits the formation of β-sheet-rich oligomers of the Alzheimer's amyloid-β(16-22) peptide. Biophys J (2011) 0.85
Coarse-grained simulations of RNA and DNA duplexes. J Phys Chem B (2013) 0.85
Molecular insights into the reversible formation of tau protein fibrils. Chem Commun (Camb) (2013) 0.84
Following the aggregation of amyloid-forming peptides by computer simulations. J Chem Phys (2005) 0.84
Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations. J Chem Phys (2010) 0.84
Intrinsic determinants of Aβ(12-24) pH-dependent self-assembly revealed by combined computational and experimental studies. PLoS One (2011) 0.83
The conversion of helix H2 to beta-sheet is accelerated in the monomer and dimer of the prion protein upon T183A mutation. J Phys Chem B (2009) 0.83
Effect of the English familial disease mutation (H6R) on the monomers and dimers of Aβ40 and Aβ42. ACS Chem Neurosci (2014) 0.83
Kinetic activation-relaxation technique. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.83
Energy landscapes of the monomer and dimer of the Alzheimer's peptide Abeta(1-28). J Chem Phys (2008) 0.82
All-atom stability and oligomerization simulations of polyglutamine nanotubes with and without the 17-amino-acid N-terminal fragment of the Huntingtin protein. J Phys Chem B (2012) 0.82
Structural characterization of VGVAPG, an elastin-derived peptide. Biopolymers (2004) 0.82
Induced beta-barrel formation of the Alzheimer's Abeta25-35 oligomers on carbon nanotube surfaces: implication for amyloid fibril inhibition. Biophys J (2009) 0.82
Single mutations in tau modulate the populations of fibril conformers through seed selection. Angew Chem Int Ed Engl (2014) 0.82
Communication: Simulated tempering with fast on-the-fly weight determination. J Chem Phys (2013) 0.82
Understanding amyloid fibril nucleation and aβ oligomer/drug interactions from computer simulations. Acc Chem Res (2013) 0.81