Published in Proc Natl Acad Sci U S A on May 03, 2004
AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides. BMC Bioinformatics (2007) 3.02
Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat Methods (2010) 2.74
General structural motifs of amyloid protofilaments. Proc Natl Acad Sci U S A (2006) 1.72
Intermolecular structure determination of amyloid fibrils with magic-angle spinning and dynamic nuclear polarization NMR. J Am Chem Soc (2011) 1.54
Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils. J Am Chem Soc (2016) 1.49
A systematic screen of beta(2)-microglobulin and insulin for amyloid-like segments. Proc Natl Acad Sci U S A (2006) 1.49
Computer-aided antibody design. Protein Eng Des Sel (2012) 1.44
The amyloid stretch hypothesis: recruiting proteins toward the dark side. Proc Natl Acad Sci U S A (2005) 1.41
Prediction of "hot spots" of aggregation in disease-linked polypeptides. BMC Struct Biol (2005) 1.34
Folding of Cu/Zn superoxide dismutase suggests structural hotspots for gain of neurotoxic function in ALS: parallels to precursors in amyloid disease. Proc Natl Acad Sci U S A (2006) 1.31
Rational design of aggregation-resistant bioactive peptides: reengineering human calcitonin. Proc Natl Acad Sci U S A (2005) 1.31
High-resolution MAS NMR analysis of PI3-SH3 amyloid fibrils: backbone conformation and implications for protofilament assembly and structure . Biochemistry (2010) 1.24
Experimental characterization of disordered and ordered aggregates populated during the process of amyloid fibril formation. Proc Natl Acad Sci U S A (2009) 1.21
Molecular determinants of the aggregation behavior of alpha- and beta-synuclein. Protein Sci (2008) 1.17
Oligomerization of amyloid Abeta16-22 peptides using hydrogen bonds and hydrophobicity forces. Biophys J (2004) 1.16
Prediction of amyloid fibril-forming segments based on a support vector machine. BMC Bioinformatics (2009) 1.16
Sequence determinants of protein aggregation: tools to increase protein solubility. Microb Cell Fact (2005) 1.09
A consensus method for the prediction of 'aggregation-prone' peptides in globular proteins. PLoS One (2013) 1.08
Microbial manipulation of the amyloid fold. Res Microbiol (2012) 0.98
Amyloid-Forming Properties of Human Apolipoproteins: Sequence Analyses and Structural Insights. Adv Exp Med Biol (2015) 0.98
The distribution of residues in a polypeptide sequence is a determinant of aggregation optimized by evolution. Biophys J (2007) 0.95
Amyloidogenic regions and interaction surfaces overlap in globular proteins related to conformational diseases. PLoS Comput Biol (2009) 0.94
Hacking the code of amyloid formation: the amyloid stretch hypothesis. Prion (2007) 0.93
Ile-phe dipeptide self-assembly: clues to amyloid formation. Biophys J (2006) 0.93
An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins. PLoS Comput Biol (2011) 0.92
What makes a protein sequence a prion? PLoS Comput Biol (2015) 0.92
Characterization of hydrophobic residue requirements for alpha-synuclein fibrillization. Biochemistry (2009) 0.92
Amyloidogenic sequences in native protein structures. Protein Sci (2010) 0.91
Protein aggregation profile of the bacterial cytosol. PLoS One (2010) 0.90
The structure of a folding intermediate provides insight into differences in immunoglobulin amyloidogenicity. Proc Natl Acad Sci U S A (2008) 0.88
On the role of aggregation prone regions in protein evolution, stability, and enzymatic catalysis: insights from diverse analyses. PLoS Comput Biol (2013) 0.85
Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure. Protein Sci (2006) 0.84
Waltz, an exciting new move in amyloid prediction. Nat Methods (2010) 0.84
Beta structure motifs of islet amyloid polypeptides identified through surface-mediated assemblies. Proc Natl Acad Sci U S A (2011) 0.84
Genesis of tramsmissible protein states via deformed templating. Prion (2012) 0.84
MetAmyl: a METa-predictor for AMYLoid proteins. PLoS One (2013) 0.84
Amyloid-like protein inclusions in tobacco transgenic plants. PLoS One (2010) 0.84
Increased Aggregation Is More Frequently Associated to Human Disease-Associated Mutations Than to Neutral Polymorphisms. PLoS Comput Biol (2015) 0.83
The structure of a fibril-forming sequence, NNQQNY, in the context of a globular fold. Protein Sci (2008) 0.83
Mapping the conformational dynamics and pathways of spontaneous steric zipper Peptide oligomerization. PLoS One (2011) 0.82
NMR characterizations of an amyloidogenic conformational ensemble of the PI3K SH3 domain. Protein Sci (2006) 0.82
Characterization of Amyloid Cores in Prion Domains. Sci Rep (2016) 0.81
Protein folding pathology in domestic animals. J Zhejiang Univ Sci (2004) 0.81
Secondary nucleating sequences affect kinetics and thermodynamics of tau aggregation. Biochemistry (2011) 0.81
NMR evidence for forming highly populated helical conformations in the partially folded hNck2 SH3 domain. Biophys J (2008) 0.81
Staphylococcal Bap Proteins Build Amyloid Scaffold Biofilm Matrices in Response to Environmental Signals. PLoS Pathog (2016) 0.80
Amyloid formation by human carboxypeptidase D transthyretin-like domain under physiological conditions. J Biol Chem (2014) 0.78
The Rho Termination Factor of Clostridium botulinum Contains a Prion-Like Domain with a Highly Amyloidogenic Core. Front Microbiol (2016) 0.78
Electrostatic effects in the folding of the SH3 domain of the c-Src tyrosine kinase: pH-dependence in 3D-domain swapping and amyloid formation. PLoS One (2014) 0.77
The N-terminal helix controls the transition between the soluble and amyloid states of an FF domain. PLoS One (2013) 0.77
Protein aggregation profile of the human kinome. Front Physiol (2012) 0.77
Association between foldability and aggregation propensity in small disulfide-rich proteins. Antioxid Redox Signal (2014) 0.76
Switch region for pathogenic structural change in conformational disease and its prediction. PLoS One (2010) 0.75
Aggregation propensity of neuronal receptors: potential implications in neurodegenerative disorders. Future Sci OA (2015) 0.75
Structural hot spots for the solubility of globular proteins. Nat Commun (2016) 0.75
Sequence-Specific Protein Aggregation Generates Defined Protein Knockdowns in Plants. Plant Physiol (2016) 0.75
The C-terminus hot spot region helps in the fibril formation of bacteriophage-associated hyaluronate lyase (HylP2). Sci Rep (2015) 0.75
The importance of a gatekeeper residue on the aggregation of transthyretin: implications for transthyretin-related amyloidoses. J Biol Chem (2014) 0.75
Cellular Regulation of Amyloid Formation in Aging and Disease. Front Neurosci (2017) 0.75
Aggregation gatekeeper and controlled assembly of Trpzip β-hairpins. Biochemistry (2014) 0.75
Characterization of Soft Amyloid Cores in Human Prion-Like Proteins. Sci Rep (2017) 0.75
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers (1983) 99.69
SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A (1998) 36.83
Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science (2003) 18.18
SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res (1999) 11.33
Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature (2002) 10.81
Protein misfolding, evolution and disease. Trends Biochem Sci (1999) 7.73
The alternative conformations of amyloidogenic proteins and their multi-step assembly pathways. Curr Opin Struct Biol (1998) 5.20
Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature (2003) 4.98
Amyloid fibrillogenesis: themes and variations. Curr Opin Struct Biol (2000) 4.76
Designing conditions for in vitro formation of amyloid protofilaments and fibrils. Proc Natl Acad Sci U S A (1999) 4.71
Elucidating the folding problem of helical peptides using empirical parameters. Nat Struct Biol (1994) 4.66
Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation. Proc Natl Acad Sci U S A (2002) 4.66
Amyloid fibrils from muscle myoglobin. Nature (2001) 3.93
Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing. EMBO J (1999) 3.72
The structural basis of protein folding and its links with human disease. Philos Trans R Soc Lond B Biol Sci (2001) 3.65
Amyloid fibril formation by an SH3 domain. Proc Natl Acad Sci U S A (1998) 3.55
Assembly of tau protein into Alzheimer paired helical filaments depends on a local sequence motif ((306)VQIVYK(311)) forming beta structure. Proc Natl Acad Sci U S A (2000) 3.49
Measurement of the beta-sheet-forming propensities of amino acids. Nature (1994) 3.36
Quantitative evaluation of congo red binding to amyloid-like proteins with a beta-pleated sheet conformation. J Histochem Cytochem (1989) 3.26
Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers (1997) 2.86
Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. J Mol Biol (1998) 2.78
Sequence determinants of amyloid fibril formation. Proc Natl Acad Sci U S A (2003) 2.71
De novo designed peptide-based amyloid fibrils. Proc Natl Acad Sci U S A (2002) 2.59
De novo amyloid proteins from designed combinatorial libraries. Proc Natl Acad Sci U S A (1999) 2.38
Kinetic partitioning of protein folding and aggregation. Nat Struct Biol (2002) 2.37
Identification of a penta- and hexapeptide of islet amyloid polypeptide (IAPP) with amyloidogenic and cytotoxic properties. J Mol Biol (2000) 2.34
Mutations and off-pathway aggregation of proteins. Trends Biotechnol (1994) 2.31
Solution structure and ligand-binding site of the SH3 domain of the p85 alpha subunit of phosphatidylinositol 3-kinase. Cell (1993) 2.20
Prediction of the absolute aggregation rates of amyloidogenic polypeptide chains. J Mol Biol (2004) 2.14
Prediction of amyloid fibril-forming proteins. J Biol Chem (2000) 2.12
Amyloidosis. Histopathology (1994) 2.10
Prolines and amyloidogenicity in fragments of the Alzheimer's peptide beta/A4. Biochemistry (1995) 2.05
Mutations that reduce aggregation of the Alzheimer's Abeta42 peptide: an unbiased search for the sequence determinants of Abeta amyloidogenesis. J Mol Biol (2002) 1.97
Studies of the aggregation of mutant proteins in vitro provide insights into the genetics of amyloid diseases. Proc Natl Acad Sci U S A (2002) 1.80
Designed protein tetramer zipped together with a hydrophobic Alzheimer homology: a structural clue to amyloid assembly. Proc Natl Acad Sci U S A (2000) 1.76
Getting out of shape. Nature (2002) 1.71
A systematic exploration of the influence of the protein stability on amyloid fibril formation in vitro. Proc Natl Acad Sci U S A (2000) 1.70
Formation of amyloid-like fibrils by self-association of a partially unfolded fibronectin type III module. J Mol Biol (1998) 1.69
Dependence on solution conditions of aggregation and amyloid formation by an SH3 domain. J Mol Biol (2001) 1.64
Therapeutic strategies for human amyloid diseases. Nat Rev Drug Discov (2002) 1.63
Rationally designed mutations convert de novo amyloid-like fibrils into monomeric beta-sheet proteins. Proc Natl Acad Sci U S A (2002) 1.62
Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis. J Mol Biol (2000) 1.55
Exploring amyloid formation by a de novo design. Proc Natl Acad Sci U S A (2004) 1.55
Molecular dynamics simulations of protein folding from the transition state. Proc Natl Acad Sci U S A (2002) 1.51
The identification of conserved interactions within the SH3 domain by alignment of sequences and structures. Protein Sci (2000) 1.50
Protein engineering as a strategy to avoid formation of amyloid fibrils. Protein Sci (2000) 1.46
Altered aggregation properties of mutant gamma-crystallins cause inherited cataract. EMBO J (2002) 1.35
Long-range order in the src SH3 folding transition state. Proc Natl Acad Sci U S A (2000) 1.31
Calculation of mutational free energy changes in transition states for protein folding. Biophys J (2003) 1.27
Protein folding and disease: a view from the first Horizon Symposium. Nat Rev Drug Discov (2003) 1.27
Medin: an integral fragment of aortic smooth muscle cell-produced lactadherin forms the most common human amyloid. Proc Natl Acad Sci U S A (1999) 1.24
Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues. Protein Sci (2001) 1.24
Preparation and characterization of purified amyloid fibrils. J Am Chem Soc (2001) 1.15
Medicine: danger--misfolding proteins. Nature (2002) 1.11
pH dependence of the reversible and irreversible thermal denaturation of gamma interferons. Biochemistry (1989) 1.00
Insights into the origin of the tendency of the PI3-SH3 domain to form amyloid fibrils. J Mol Biol (2002) 1.00
Mutational effects on inclusion body formation. Adv Protein Chem (1997) 0.99
Non-native local interactions in protein folding and stability: introducing a helical tendency in the all beta-sheet alpha-spectrin SH3 domain. J Mol Biol (1997) 0.94
The changing concepts of amyloid. Arch Pathol Lab Med (2001) 0.83
Sequence optimization for native state stability determines the evolution and folding kinetics of a small protein. J Mol Biol (2003) 0.80
Competing intrachain interactions regulate the formation of beta-sheet fibrils in bovine PrP peptides. Protein Sci (2003) 0.80
Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem (2006) 22.87
Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature (2002) 10.81
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol (2002) 9.74
Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat Biotechnol (2007) 8.88
Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol (2004) 7.02
The FoldX web server: an online force field. Nucleic Acids Res (2005) 6.30
Simultaneous determination of protein structure and dynamics. Nature (2005) 5.28
Protein aggregation and aggregate toxicity: new insights into protein folding, misfolding diseases and biological evolution. J Mol Med (Berl) (2003) 5.15
Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature (2003) 4.98
The intestinal stem cell signature identifies colorectal cancer stem cells and predicts disease relapse. Cell Stem Cell (2011) 4.79
Transcriptome complexity in a genome-reduced bacterium. Science (2009) 4.64
Correlation of mRNA and protein in complex biological samples. FEBS Lett (2009) 4.38
The protofilament structure of insulin amyloid fibrils. Proc Natl Acad Sci U S A (2002) 4.08
Long-range interactions within a nonnative protein. Science (2002) 4.06
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci U S A (2007) 3.96
An analytical solution to the kinetics of breakable filament assembly. Science (2009) 3.87
Amyloid formation by globular proteins under native conditions. Nat Chem Biol (2009) 3.72
High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy. Proc Natl Acad Sci U S A (2004) 3.58
Impact of genome reduction on bacterial metabolism and its regulation. Science (2009) 3.45
Evolvability and hierarchy in rewired bacterial gene networks. Nature (2008) 3.43
Direct observation of the interconversion of normal and toxic forms of α-synuclein. Cell (2012) 3.39
Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol (2005) 3.28
Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases. J Mol Biol (2005) 3.18
Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations. J Am Chem Soc (2005) 3.13
Anoikis: a necessary death program for anchorage-dependent cells. Biochem Pharmacol (2008) 2.96
Dependency of colorectal cancer on a TGF-β-driven program in stromal cells for metastasis initiation. Cancer Cell (2012) 2.94
Role of intermolecular forces in defining material properties of protein nanofibrils. Science (2007) 2.94
Proliferation of amyloid-β42 aggregates occurs through a secondary nucleation mechanism. Proc Natl Acad Sci U S A (2013) 2.89
Structure-based assembly of protein complexes in yeast. Science (2004) 2.89
Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR. Nature (2004) 2.84
Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat Methods (2010) 2.74
From in vivo to in silico biology and back. Nature (2006) 2.74
Sequence determinants of amyloid fibril formation. Proc Natl Acad Sci U S A (2003) 2.71
The importance of sequence diversity in the aggregation and evolution of proteins. Nature (2005) 2.70
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acids Res (2005) 2.69
Noise in transcription negative feedback loops: simulation and experimental analysis. Mol Syst Biol (2006) 2.69
De novo determination of peptide structure with solid-state magic-angle spinning NMR spectroscopy. Proc Natl Acad Sci U S A (2002) 2.66
De novo designed peptide-based amyloid fibrils. Proc Natl Acad Sci U S A (2002) 2.59
The behaviour of polyamino acids reveals an inverse side chain effect in amyloid structure formation. EMBO J (2002) 2.59
Prediction of aggregation-prone regions in structured proteins. J Mol Biol (2008) 2.56
Control of Drosophila gastrulation by apical localization of adherens junctions and RhoGEF2. Science (2007) 2.51
A causative link between the structure of aberrant protein oligomers and their toxicity. Nat Chem Biol (2010) 2.48
Characterization of the nanoscale properties of individual amyloid fibrils. Proc Natl Acad Sci U S A (2006) 2.46
How protein stability and new functions trade off. PLoS Comput Biol (2008) 2.41
Molecular recycling within amyloid fibrils. Nature (2005) 2.39
Kinetic partitioning of protein folding and aggregation. Nat Struct Biol (2002) 2.37
Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature (2008) 2.37
Systematic in vivo analysis of the intrinsic determinants of amyloid Beta pathogenicity. PLoS Biol (2007) 2.35
Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc Natl Acad Sci U S A (2005) 2.31
Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol (2011) 2.31
The stability effects of protein mutations appear to be universally distributed. J Mol Biol (2007) 2.25
Reciprocal metabolic reprogramming through lactate shuttle coordinately influences tumor-stroma interplay. Cancer Res (2012) 2.20
Molecular conformation of a peptide fragment of transthyretin in an amyloid fibril. Proc Natl Acad Sci U S A (2002) 2.18
Multiple tight phospholipid-binding modes of alpha-synuclein revealed by solution NMR spectroscopy. J Mol Biol (2009) 2.14
Prediction of the absolute aggregation rates of amyloidogenic polypeptide chains. J Mol Biol (2004) 2.14
Protein aggregation and amyloidosis: confusion of the kinds? Curr Opin Struct Biol (2006) 2.10
Anoikis molecular pathways and its role in cancer progression. Biochim Biophys Acta (2013) 2.08
Reactive oxygen species as essential mediators of cell adhesion: the oxidative inhibition of a FAK tyrosine phosphatase is required for cell adhesion. J Cell Biol (2003) 2.05
A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins. J Mol Biol (2004) 2.05
Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J Mol Biol (2005) 2.04
Analysis and description of HOLTIN service provision for AECG monitoring in complex indoor environments. Sensors (Basel) (2013) 2.02
Myoglobin forms amyloid fibrils by association of unfolded polypeptide segments. Proc Natl Acad Sci U S A (2003) 1.93
Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci (2005) 1.91
How evolutionary pressure against protein aggregation shaped chaperone specificity. J Mol Biol (2005) 1.91
Computer-aided design of a PDZ domain to recognize new target sequences. Nat Struct Biol (2002) 1.89
Prefibrillar amyloid aggregates could be generic toxins in higher organisms. J Neurosci (2006) 1.89
Life on the edge: a link between gene expression levels and aggregation rates of human proteins. Trends Biochem Sci (2007) 1.88
Studies of the aggregation of mutant proteins in vitro provide insights into the genetics of amyloid diseases. Proc Natl Acad Sci U S A (2002) 1.80
The extracellular chaperone clusterin influences amyloid formation and toxicity by interacting with prefibrillar structures. FASEB J (2007) 1.79
Prefibrillar amyloid protein aggregates share common features of cytotoxicity. J Biol Chem (2004) 1.79
Prevention of amyloid-like aggregation as a driving force of protein evolution. EMBO Rep (2007) 1.78
Recognizing and defining true Ras binding domains I: biochemical analysis. J Mol Biol (2005) 1.76
Atomic structure and hierarchical assembly of a cross-β amyloid fibril. Proc Natl Acad Sci U S A (2013) 1.75
Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences. Nucleic Acids Res (2008) 1.74
Stabilization of neurotoxic Alzheimer amyloid-beta oligomers by protein engineering. Proc Natl Acad Sci U S A (2010) 1.72
From macroscopic measurements to microscopic mechanisms of protein aggregation. J Mol Biol (2012) 1.71
Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils. PLoS Comput Biol (2007) 1.71
Active gamma-secretase complexes contain only one of each component. J Biol Chem (2007) 1.69
Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. Genome Res (2009) 1.68
A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme. Nature (2003) 1.66
Local cooperativity in the unfolding of an amyloidogenic variant of human lysozyme. Nat Struct Biol (2002) 1.64
Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol (2006) 1.64
Glycine residues appear to be evolutionarily conserved for their ability to inhibit aggregation. Structure (2005) 1.63