Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations.

Direct detection of transient alpha-helical states in islet amyloid polypeptide. Protein Sci (2006) 1.74

Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils. PLoS Comput Biol (2007) 1.71

The amyloid stretch hypothesis: recruiting proteins toward the dark side. Proc Natl Acad Sci U S A (2005) 1.41

Stability and structure of oligomers of the Alzheimer peptide Abeta16-22: from the dimer to the 32-mer. Biophys J (2006) 1.07

Molecular dynamics simulations on the oligomer-formation process of the GNNQQNY peptide from yeast prion protein Sup35. Biophys J (2007) 1.05

The importance of micelle-bound states for the bioactivities of bifunctional peptide derivatives for delta/mu opioid receptor agonists and neurokinin 1 receptor antagonists. J Med Chem (2008) 1.02

Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment. PLoS Comput Biol (2008) 0.99

Molecular dynamics simulation suggests possible interaction patterns at early steps of beta2-microglobulin aggregation. Biophys J (2006) 0.96

Thermodynamic selection of steric zipper patterns in the amyloid cross-beta spine. PLoS Comput Biol (2009) 0.96

Investigating the mechanism of peptide aggregation: insights from mixed monte carlo-molecular dynamics simulations. Biophys J (2008) 0.95

9,10-Anthraquinone hinders beta-aggregation: how does a small molecule interfere with Abeta-peptide amyloid fibrillation? Protein Sci (2009) 0.94

Computational simulations of the early steps of protein aggregation. Prion (2007) 0.92

All-atom computer simulations of amyloid fibrils disaggregation. Biophys J (2008) 0.86

Free cholesterol induces higher β-sheet content in Aβ peptide oligomers by aromatic interaction with Phe19. PLoS One (2012) 0.83

Mapping the conformational dynamics and pathways of spontaneous steric zipper Peptide oligomerization. PLoS One (2011) 0.82

Fibrillization propensity for short designed hexapeptides predicted by computer simulation. J Mol Biol (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

Structural elements regulating amyloidogenesis: a cholinesterase model system. PLoS One (2008) 0.80

Interplay of sequence, topology and termini charge in determining the stability of the aggregates of GNNQQNY mutants: a molecular dynamics study. PLoS One (2014) 0.75

Discriminant analysis of prion sequences for prediction of susceptibility. Exp Mol Med (2013) 0.75

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

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

Proteome organization in a genome-reduced bacterium. Science (2009) 3.97

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

Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol (2005) 3.28

Structure-based assembly of protein complexes in yeast. Science (2004) 2.89

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

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 designed peptide-based amyloid fibrils. Proc Natl Acad Sci U S A (2002) 2.59

Control of Drosophila gastrulation by apical localization of adherens junctions and RhoGEF2. Science (2007) 2.51

How protein stability and new functions trade off. PLoS Comput Biol (2008) 2.41

Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature (2008) 2.37

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

Swe1Wee1-dependent tyrosine phosphorylation of Hsp90 regulates distinct facets of chaperone function. Mol Cell (2010) 2.24

Protein aggregation and amyloidosis: confusion of the kinds? Curr Opin Struct Biol (2006) 2.10

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

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

Short amino acid stretches can mediate amyloid formation in globular proteins: the Src homology 3 (SH3) case. Proc Natl Acad Sci U S A (2004) 1.83

Recognizing and defining true Ras binding domains I: biochemical analysis. J Mol Biol (2005) 1.76

Rational design of shepherdin, a novel anticancer agent. Cancer Cell (2005) 1.74

Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences. Nucleic Acids Res (2008) 1.74

Combinatorial drug design targeting multiple cancer signaling networks controlled by mitochondrial Hsp90. J Clin Invest (2009) 1.72

Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. Genome Res (2009) 1.68

Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: a molecular dynamics study. Proc Natl Acad Sci U S A (2002) 1.64

Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol (2006) 1.64

Strand-specific deep sequencing of the transcriptome. Genome Res (2010) 1.58

A graphical interface for the FoldX forcefield. Bioinformatics (2011) 1.50

Engineering gene networks to emulate Drosophila embryonic pattern formation. PLoS Biol (2005) 1.48

Designed tumor necrosis factor-related apoptosis-inducing ligand variants initiating apoptosis exclusively via the DR5 receptor. Proc Natl Acad Sci U S A (2006) 1.45

Exploiting the Burkholderia pseudomallei acute phase antigen BPSL2765 for structure-based epitope discovery/design in structural vaccinology. Chem Biol (2013) 1.45

Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol (2012) 1.44

Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer. PLoS Comput Biol (2009) 1.43

A detailed thermodynamic analysis of ras/effector complex interfaces. J Mol Biol (2004) 1.42

The amyloid stretch hypothesis: recruiting proteins toward the dark side. Proc Natl Acad Sci U S A (2005) 1.41

Energy estimation in protein design. Curr Opin Struct Biol (2002) 1.39

Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol (2011) 1.39

PepX: a structural database of non-redundant protein-peptide complexes. Nucleic Acids Res (2009) 1.35

Towards cellular systems in 4D. Cell (2005) 1.33

Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations. J Mol Biol (2005) 1.33

Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PLoS Genet (2013) 1.32

Analyzing protein interaction networks using structural information. Annu Rev Biochem (2008) 1.32

Design of a wearable device for ECG continuous monitoring using wireless technology. Conf Proc IEEE Eng Med Biol Soc (2004) 1.28

Calculation of mutational free energy changes in transition states for protein folding. Biophys J (2003) 1.27

Space as the final frontier in stochastic simulations of biological systems. FEBS Lett (2005) 1.25

Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases. Am J Hum Genet (2007) 1.24

Engineering signal transduction pathways. Cell (2010) 1.21

Computational design of peptide ligands. Trends Biotechnol (2011) 1.19

Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus. Nucleic Acids Res (2010) 1.19

Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics. Proteins (2005) 1.18

Unspecific hydrophobic stabilization of folding transition states. Proc Natl Acad Sci U S A (2002) 1.16

Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example. Nucleic Acids Res (2010) 1.16

Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants. Nucleic Acids Res (2011) 1.15

Computer modelling in combination with in vitro studies reveals similar binding affinities of Drosophila Crumbs for the PDZ domains of Stardust and DmPar-6. Eur J Cell Biol (2006) 1.15

Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions. PLoS Comput Biol (2005) 1.15

Advancing cell biology through proteomics in space and time (PROSPECTS). Mol Cell Proteomics (2012) 1.15

The multiple-specificity landscape of modular peptide recognition domains. Mol Syst Biol (2011) 1.14

Personalized respiratory medicine: exploring the horizon, addressing the issues. Summary of a BRN-AJRCCM workshop held in Barcelona on June 12, 2014. Am J Respir Crit Care Med (2015) 1.12

Cell type-specific importance of ras-c-raf complex association rate constants for MAPK signaling. Sci Signal (2009) 1.12

Structures in systems biology. Curr Opin Struct Biol (2007) 1.11

Analysis of disease-linked rhodopsin mutations based on structure, function, and protein stability calculations. J Mol Biol (2010) 1.10

Human epidermal stem cell function is regulated by circadian oscillations. Cell Stem Cell (2013) 1.09

Beta-hairpin conformation of fibrillogenic peptides: structure and alpha-beta transition mechanism revealed by molecular dynamics simulations. Proteins (2004) 1.09

The ubiquitin domain superfold: structure-based sequence alignments and characterization of binding epitopes. J Mol Biol (2005) 1.08

Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories. J Comput Chem (2008) 1.07

Antileukemic activity of shepherdin and molecular diversity of hsp90 inhibitors. J Natl Cancer Inst (2006) 1.06

Conformational strain in the hydrophobic core and its implications for protein folding and design. Nat Struct Biol (2002) 1.06

Localized transfection on arrays of magnetic beads coated with PCR products. Nat Methods (2005) 1.06

Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure. BMC Struct Biol (2008) 1.05

Transcription start site associated RNAs in bacteria. Mol Syst Biol (2012) 1.04

Strategies for protein synthetic biology. Nucleic Acids Res (2010) 1.04

Reconstruction of protein backbones from the BriX collection of canonical protein fragments. PLoS Comput Biol (2008) 1.04

Protein-peptide interactions adopt the same structural motifs as monomeric protein folds. Structure (2009) 1.04

Small-molecule targeting of heat shock protein 90 chaperone function: rational identification of a new anticancer lead. J Med Chem (2006) 1.03

Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm. PLoS Comput Biol (2008) 1.02

Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. Proc Natl Acad Sci U S A (2008) 1.01

Corresponding functional dynamics across the Hsp90 Chaperone family: insights from a multiscale analysis of MD simulations. PLoS Comput Biol (2012) 1.01

High frequency of germline succinate dehydrogenase mutations in sporadic cervical paragangliomas in northern Spain: mitochondrial succinate dehydrogenase structure-function relationships and clinical-pathological correlations. J Clin Endocrinol Metab (2007) 1.01

DR4-selective tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) variants obtained by structure-based design. J Biol Chem (2008) 1.01

Understanding the determinants of stability and folding of small globular proteins from their energetics. Protein Sci (2004) 1.00

Insights into the origin of the tendency of the PI3-SH3 domain to form amyloid fibrils. J Mol Biol (2002) 1.00

Dynamic diagnosis of familial prion diseases supports the β2-α2 loop as a universal interference target. PLoS One (2011) 0.98

BriX: a database of protein building blocks for structural analysis, modeling and design. Nucleic Acids Res (2010) 0.98

Effect of hexafluoroisopropanol alcohol on the structure of melittin: a molecular dynamics simulation study. Protein Sci (2005) 0.97

Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations. PLoS Comput Biol (2012) 0.97

The tryptophan switch: changing ligand-binding specificity from type I to type II in SH3 domains. J Mol Biol (2004) 0.96

Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins. Proteins (2008) 0.96