Published in Curr Opin Chem Biol on August 28, 2006
Folding versus aggregation: polypeptide conformations on competing pathways. Arch Biochem Biophys (2007) 1.97
Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils. PLoS Comput Biol (2007) 1.71
Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev (2010) 1.62
Amyloid beta-protein monomer folding: free-energy surfaces reveal alloform-specific differences. J Mol Biol (2008) 1.62
Nanostructure and molecular mechanics of spider dragline silk protein assemblies. J R Soc Interface (2010) 1.46
Computer-aided antibody design. Protein Eng Des Sel (2012) 1.44
Cooperative hydrogen bonding in amyloid formation. Protein Sci (2007) 1.33
Replica exchange simulations of the thermodynamics of Abeta fibril growth. Biophys J (2009) 1.18
Polymorphism of Alzheimer's Abeta17-42 (p3) oligomers: the importance of the turn location and its conformation. Biophys J (2009) 1.13
Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42. J Phys Chem B (2008) 1.10
Characterization of the nucleation barriers for protein aggregation and amyloid formation. HFSP J (2007) 1.04
Probing the effect of amino-terminal truncation for Abeta1-40 peptides. J Phys Chem B (2009) 1.04
Interpeptide interactions induce helix to strand structural transition in Abeta peptides. Proteins (2009) 0.99
Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment. PLoS Comput Biol (2008) 0.99
Probing energetics of Abeta fibril elongation by molecular dynamics simulations. Biophys J (2009) 0.98
Structural characterization of GNNQQNY amyloid fibrils by magic angle spinning NMR. Biochemistry (2010) 0.96
Extending the PRIME model for protein aggregation to all 20 amino acids. Proteins (2010) 0.96
Thermodynamic description of polymorphism in Q- and N-rich peptide aggregates revealed by atomistic simulation. Biophys J (2009) 0.95
Mapping conformational ensembles of aβ oligomers in molecular dynamics simulations. Biophys J (2010) 0.94
Computational simulations of the early steps of protein aggregation. Prion (2007) 0.92
Self-assembly of phenylalanine oligopeptides: insights from experiments and simulations. Biophys J (2009) 0.92
Structure and dynamics of amyloid-β segmental polymorphisms. PLoS One (2012) 0.91
Molecular dynamics simulations of Ibuprofen binding to Abeta peptides. Biophys J (2009) 0.91
Polymorphic triple beta-sheet structures contribute to amide hydrogen/deuterium (H/D) exchange protection in the Alzheimer amyloid beta42 peptide. J Biol Chem (2011) 0.91
Are current atomistic force fields accurate enough to study proteins in crowded environments? PLoS Comput Biol (2014) 0.90
Spontaneous formation of twisted Aβ(16-22) fibrils in large-scale molecular-dynamics simulations. Biophys J (2011) 0.90
Temperature-induced dissociation of Abeta monomers from amyloid fibril. Biophys J (2008) 0.89
What determines the structure and stability of KFFE monomers, dimers, and protofibrils? Biophys J (2009) 0.89
Conformational stability of fibrillar amyloid-beta oligomers via protofilament pair formation - a systematic computational study. PLoS One (2013) 0.88
Fibril elongation by Aβ(17-42): kinetic network analysis of hybrid-resolution molecular dynamics simulations. J Am Chem Soc (2014) 0.87
All-atom computer simulations of amyloid fibrils disaggregation. Biophys J (2008) 0.86
Probing protein aggregation using discrete molecular dynamics. Front Biosci (2008) 0.86
Side chain interactions can impede amyloid fibril growth: replica exchange simulations of Abeta peptide mutant. J Phys Chem B (2009) 0.85
Side-chain hydrophobicity and the stability of Aβ₁₆₋₂₂ aggregates. Protein Sci (2012) 0.85
Binding of nonsteroidal anti-inflammatory drugs to Abeta fibril. Proteins (2010) 0.85
Alzheimer's protective A2T mutation changes the conformational landscape of the Aβ₁₋₄₂ monomer differently than does the A2V mutation. Biophys J (2015) 0.84
Comparisons with amyloid-β reveal an aspartate residue that stabilizes fibrils of the aortic amyloid peptide medin. J Biol Chem (2015) 0.84
Molecular dynamics simulations of anti-aggregation effect of ibuprofen. Biophys J (2010) 0.83
Mapping the conformational dynamics and pathways of spontaneous steric zipper Peptide oligomerization. PLoS One (2011) 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
Globular state in the oligomers formed by Abeta peptides. J Chem Phys (2010) 0.82
Binding to the lipid monolayer induces conformational transition in Aβ monomer. J Mol Model (2012) 0.82
Molecular interactions of Alzheimer's biomarker FDDNP with Aβ peptide. Biophys J (2012) 0.81
Nonsteroidal anti-inflammatory drug naproxen destabilizes Aβ amyloid fibrils: a molecular dynamics investigation. J Phys Chem B (2010) 0.81
Measurement of amyloid formation by turbidity assay-seeing through the cloud. Biophys Rev (2016) 0.81
Effect of pathogenic mutations on the structure and dynamics of Alzheimer's A beta 42-amyloid oligomers. J Mol Model (2009) 0.81
Dynamic properties of pH-dependent structural organization of the amyloidogenic beta-protein (1-40). Prion (2009) 0.81
Cooperativity among short amyloid stretches in long amyloidogenic sequences. PLoS One (2012) 0.80
Structural Conversion of Aβ17-42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways. PLoS Comput Biol (2015) 0.79
Naproxen interferes with the assembly of Aβ oligomers implicated in Alzheimer's disease. Biophys J (2011) 0.79
Molecular interpretation of ACTH-β-endorphin coaggregation: relevance to secretory granule biogenesis. PLoS One (2012) 0.78
Charge effects on the fibril-forming peptide KTVIIE: a two-dimensional replica exchange simulation study. Biophys J (2012) 0.78
Structure and aggregation mechanism of beta(2)-microglobulin (83-99) peptides studied by molecular dynamics simulations. Biophys J (2007) 0.78
Computational backbone mutagenesis of Abeta peptides: probing the role of backbone hydrogen bonds in aggregation. J Phys Chem B (2010) 0.78
Interaction of amyloid inhibitor proteins with amyloid beta peptides: insight from molecular dynamics simulations. PLoS One (2014) 0.77
Studying interactions by molecular dynamics simulations at high concentration. J Biomed Biotechnol (2012) 0.76
Does amino acid sequence determine the properties of Aβ dimer? J Chem Phys (2011) 0.76
Hydralazine modifies Aβ fibril formation and prevents modification by lipids in vitro. Biochemistry (2010) 0.76
Computational approaches to understanding protein aggregation in neurodegeneration. J Mol Cell Biol (2014) 0.75
Early Events in the Amyloid Formation of the A546T Mutant of Transforming Growth Factor β-Induced Protein in Corneal Dystrophies Compared to the Nonfibrillating R555W and R555Q Mutants. Biochemistry (2015) 0.75
On the characterization of intermediates in the isodesmic aggregation pathway of hen lysozyme at alkaline pH. PLoS One (2014) 0.75
Statistical mechanical treatments of protein amyloid formation. Int J Mol Sci (2013) 0.75
Allosteric stabilization of the amyloid-β peptide hairpin by the fluctuating N-terminal. Chem Commun (Camb) (2015) 0.75
Computational Investigation into the Interactions of Traditional Chinese Medicine Molecules of WenQingYin with GluR2. Int J Mol Sci (2017) 0.75
PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res (2005) 7.66
The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol (2009) 7.36
Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins (2002) 5.79
Is allostery an intrinsic property of all dynamic proteins? Proteins (2004) 4.99
A method for simultaneous alignment of multiple protein structures. Proteins (2004) 3.45
Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci U S A (2003) 3.42
Allostery: absence of a change in shape does not imply that allostery is not at play. J Mol Biol (2008) 3.24
Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol (2004) 3.10
Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects. Proc Natl Acad Sci U S A (2002) 3.06
Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci (2002) 3.01
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci (2010) 2.97
Principles of protein-protein interactions: what are the preferred ways for proteins to interact? Chem Rev (2008) 2.96
FireDock: fast interaction refinement in molecular docking. Proteins (2007) 2.90
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64
Close-range electrostatic interactions in proteins. Chembiochem (2002) 2.42
FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res (2008) 2.39
The origin of allosteric functional modulation: multiple pre-existing pathways. Structure (2009) 2.33
Recognition of functional sites in protein structures. J Mol Biol (2004) 2.32
Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Mol Biosyst (2009) 2.18
Extended disordered proteins: targeting function with less scaffold. Trends Biochem Sci (2003) 2.12
A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci (2004) 2.11
PRISM: protein interactions by structural matching. Nucleic Acids Res (2005) 2.11
Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure (2004) 2.06
Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol Syst Biol (2006) 1.98
Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins (2003) 1.95
Geometry-based flexible and symmetric protein docking. Proteins (2005) 1.95
Flexible protein alignment and hinge detection. Proteins (2002) 1.93
Relationship between ion pair geometries and electrostatic strengths in proteins. Biophys J (2002) 1.91
HingeProt: automated prediction of hinges in protein structures. Proteins (2008) 1.86
Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc (2011) 1.84
Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J Mol Biol (2008) 1.80
Principles of flexible protein-protein docking. Proteins (2008) 1.71
ARTS: alignment of RNA tertiary structures. Bioinformatics (2005) 1.67
Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. J Mol Biol (2004) 1.64
Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev (2010) 1.62
Enzyme dynamics point to stepwise conformational selection in catalysis. Curr Opin Chem Biol (2010) 1.61
Similar binding sites and different partners: implications to shared proteins in cellular pathways. Structure (2007) 1.60
Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation. Protein Sci (2002) 1.59
Dynamic allostery: linkers are not merely flexible. Structure (2011) 1.58
Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families. Proteins (2006) 1.58
Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. J Mol Biol (2004) 1.54
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Res (2008) 1.52
Architectures and functional coverage of protein-protein interfaces. J Mol Biol (2008) 1.51
Truncated beta-amyloid peptide channels provide an alternative mechanism for Alzheimer's Disease and Down syndrome. Proc Natl Acad Sci U S A (2010) 1.48
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform (2009) 1.47
FiberDock: Flexible induced-fit backbone refinement in molecular docking. Proteins (2010) 1.47
Models of beta-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process. Biophys J (2007) 1.44
Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Biophys J (2007) 1.44
New structures help the modeling of toxic amyloidbeta ion channels. Trends Biochem Sci (2008) 1.43
Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. Proc Natl Acad Sci U S A (2005) 1.43
Atomic-level description of amyloid beta-dimer formation. J Am Chem Soc (2006) 1.41
The ARTS web server for aligning RNA tertiary structures. Nucleic Acids Res (2006) 1.37
Mechanisms of transcription factor selectivity. Trends Genet (2010) 1.35
Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophys J (2006) 1.33
Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Biophys J (2003) 1.33
Multiple structural alignment by secondary structures: algorithm and applications. Protein Sci (2003) 1.32
Allostery and population shift in drug discovery. Curr Opin Pharmacol (2010) 1.32
Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states. Proc Natl Acad Sci U S A (2010) 1.32
Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels. Biophys J (2008) 1.30
MolAxis: efficient and accurate identification of channels in macromolecules. Proteins (2008) 1.30
Nanoparticle-induced vascular blockade in human prostate cancer. Blood (2010) 1.30
The multiple common point set problem and its application to molecule binding pattern detection. J Comput Biol (2006) 1.28
Topological properties of protein interaction networks from a structural perspective. Biochem Soc Trans (2008) 1.28
Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's β by solid-state NMR spectroscopy. J Am Chem Soc (2011) 1.27
Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach. Phys Biol (2005) 1.26
Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Sci (2006) 1.26
How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding. J Mol Biol (2006) 1.26
A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. BMC Bioinformatics (2011) 1.25
FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking. Nucleic Acids Res (2010) 1.25
Predicting molecular interactions in silico: II. Protein-protein and protein-drug docking. Curr Med Chem (2004) 1.25
PRISM: protein-protein interaction prediction by structural matching. Methods Mol Biol (2008) 1.24
Protein-protein interaction networks: how can a hub protein bind so many different partners? Trends Biochem Sci (2009) 1.24
Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism. J Phys Chem B (2009) 1.23
Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets. Nucleic Acids Res (2007) 1.22
Spatial chemical conservation of hot spot interactions in protein-protein complexes. BMC Biol (2007) 1.22
β-Barrel topology of Alzheimer's β-amyloid ion channels. J Mol Biol (2010) 1.21
How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophys J (2004) 1.21
SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res (2005) 1.20
Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages. Genome Biol (2007) 1.20
Analysis and classification of RNA tertiary structures. RNA (2008) 1.20
Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design. Proc Natl Acad Sci U S A (2008) 1.20
Interaction of protegrin-1 with lipid bilayers: membrane thinning effect. Biophys J (2006) 1.18
Misfolded amyloid ion channels present mobile beta-sheet subunits in contrast to conventional ion channels. Biophys J (2009) 1.18
Antimicrobial protegrin-1 forms amyloid-like fibrils with rapid kinetics suggesting a functional link. Biophys J (2011) 1.17
SiteLight: binding-site prediction using phage display libraries. Protein Sci (2003) 1.17
From structure to function: methods and applications. Curr Protein Pept Sci (2005) 1.16
Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design. Curr Top Med Chem (2007) 1.16
PharmaGist: a webserver for ligand-based pharmacophore detection. Nucleic Acids Res (2008) 1.16
Hollow core of Alzheimer's Abeta42 amyloid observed by cryoEM is relevant at physiological pH. Proc Natl Acad Sci U S A (2010) 1.14
Automatic prediction of protein interactions with large scale motion. Proteins (2007) 1.13
Polymorphism of Alzheimer's Abeta17-42 (p3) oligomers: the importance of the turn location and its conformation. Biophys J (2009) 1.13
EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution cryo-EM maps. IEEE/ACM Trans Comput Biol Bioinform (2007) 1.12
Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design. J Chem Inf Model (2008) 1.12
Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways. Protein Eng Des Sel (2005) 1.12
Approaching the CAPRI challenge with an efficient geometry-based docking. Proteins (2005) 1.12
Atomic force microscopy and MD simulations reveal pore-like structures of all-D-enantiomer of Alzheimer's β-amyloid peptide: relevance to the ion channel mechanism of AD pathology. J Phys Chem B (2012) 1.11
Protein structure prediction via combinatorial assembly of sub-structural units. Bioinformatics (2003) 1.11
The hydrophobic effect: a new insight from cold denaturation and a two-state water structure. Crit Rev Biochem Mol Biol (2002) 1.10
Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42. J Phys Chem B (2008) 1.10
MolAxis: a server for identification of channels in macromolecules. Nucleic Acids Res (2008) 1.10