Co-evolutionary analysis reveals insights into protein-protein interactions.

Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol (2007) 3.46

Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol (2007) 2.72

Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci U S A (2005) 2.69

Assessing the limits of genomic data integration for predicting protein networks. Genome Res (2005) 2.33

Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A (2004) 1.96

Protein co-evolution, co-adaptation and interactions. EMBO J (2008) 1.65

Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol (2006) 1.60

Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics (2007) 1.47

COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. Bioinformatics (2006) 1.41

Specificity in protein interactions and its relationship with sequence diversity and coevolution. Proc Natl Acad Sci U S A (2007) 1.39

Coevolution of interacting fertilization proteins. PLoS Genet (2009) 1.26

The mechanism of folding of Im7 reveals competition between functional and kinetic evolutionary constraints. Nat Struct Mol Biol (2009) 1.26

Predicting protein-protein interaction by searching evolutionary tree automorphism space. Bioinformatics (2005) 1.21

Why should we care about molecular coevolution? Evol Bioinform Online (2008) 1.19

Correlated evolution of interacting proteins: looking behind the mirrortree. J Mol Biol (2008) 1.12

Chapter 4: Protein interactions and disease. PLoS Comput Biol (2012) 1.10

Evolutionary rate covariation identifies new members of a protein network required for Drosophila melanogaster female post-mating responses. PLoS Genet (2014) 1.08

Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices. BMC Bioinformatics (2007) 1.08

A virus-binding hot spot on human angiotensin-converting enzyme 2 is critical for binding of two different coronaviruses. J Virol (2011) 1.03

Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis. PLoS Comput Biol (2008) 1.02

A novel method to detect proteins evolving at correlated rates: identifying new functional relationships between coevolving proteins. Mol Biol Evol (2009) 0.98

Detecting coevolution through allelic association between physically unlinked loci. Am J Hum Genet (2010) 0.97

The two authentic methionine aminopeptidase genes are differentially expressed in Bacillus subtilis. BMC Microbiol (2005) 0.95

Construction and analysis of protein-protein interaction networks. Autom Exp (2010) 0.94

Stimulus-induced S-nitrosylation of Syntaxin 4 impacts insulin granule exocytosis. J Biol Chem (2011) 0.92

Tight coevolution of proliferating cell nuclear antigen (PCNA)-partner interaction networks in fungi leads to interspecies network incompatibility. Proc Natl Acad Sci U S A (2012) 0.89

Co-evolutionary networks of genes and cellular processes across fungal species. Genome Biol (2009) 0.89

Metabolic pathways variability and sequence/networks comparisons. BMC Bioinformatics (2006) 0.87

Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines. BMC Bioinformatics (2010) 0.86

Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function. Proc Natl Acad Sci U S A (2007) 0.84

Protein interaction predictions from diverse sources. Drug Discov Today (2008) 0.84

The effects of network neighbours on protein evolution. PLoS One (2011) 0.83

Gamma chain receptor interleukins: evidence for positive selection driving the evolution of cell-to-cell communicators in the mammalian immune system. J Mol Evol (2005) 0.82

Calculation of evolutionary correlation between individual genes and full-length genome: a method useful for choosing phylogenetic markers for molecular epidemiology. PLoS One (2013) 0.80

Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation. Ann Bot (2012) 0.80

New methods to measure residues coevolution in proteins. BMC Bioinformatics (2011) 0.80

Covariation of branch lengths in phylogenies of functionally related genes. PLoS One (2009) 0.80

Global multiple protein-protein interaction network alignment by combining pairwise network alignments. BMC Bioinformatics (2015) 0.79

Protein-protein interaction map is a key gateway into liver regeneration. World J Gastroenterol (2010) 0.77

Recent coselection in human populations revealed by protein-protein interaction network. Genome Biol Evol (2014) 0.76

Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins. BMC Bioinformatics (2010) 0.76

Coevolution of axon guidance molecule Slit and its receptor Robo. PLoS One (2014) 0.76

Origin of the plant Tm-1-like gene via two independent horizontal transfer events and one gene fusion event. Sci Rep (2016) 0.76

Predicting protein-protein interaction by the mirrortree method: possibilities and limitations. PLoS One (2013) 0.76

Identifying gene interaction networks. Methods Mol Biol (2012) 0.75

Bayesian inference for genomic data integration reduces misclassification rate in predicting protein-protein interactions. PLoS Comput Biol (2011) 0.75

The Amino Acid Transporter JhI-21 Coevolves with Glutamate Receptors, Impacts NMJ Physiology, and Influences Locomotor Activity in Drosophila Larvae. Sci Rep (2016) 0.75

Synthetic mammalian prions. Science (2004) 7.35

Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol (2003) 4.24

Evidence for assembly of prions with left-handed beta-helices into trimers. Proc Natl Acad Sci U S A (2004) 3.64

GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res (2003) 3.34

Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors. Bioinformatics (2004) 3.03

Pathway complexity of prion protein assembly into amyloid. J Biol Chem (2002) 2.96

Structural studies of the scrapie prion protein by electron crystallography. Proc Natl Acad Sci U S A (2002) 2.91

Continuum of prion protein structures enciphers a multitude of prion isolate-specified phenotypes. Proc Natl Acad Sci U S A (2006) 2.69

Strain-specified characteristics of mouse synthetic prions. Proc Natl Acad Sci U S A (2005) 2.25

Protease-sensitive synthetic prions. PLoS Pathog (2010) 2.14

Searching for new antimalarial therapeutics amongst known drugs. Chem Biol Drug Des (2006) 2.10

Mutant PrPSc conformers induced by a synthetic peptide and several prion strains. J Virol (2004) 2.07

Natural and synthetic prion structure from X-ray fiber diffraction. Proc Natl Acad Sci U S A (2009) 1.97

Apolipoprotein (apo) E4 enhances amyloid beta peptide production in cultured neuronal cells: apoE structure as a potential therapeutic target. Proc Natl Acad Sci U S A (2005) 1.91

Dominant-negative inhibition of prion replication in transgenic mice. Proc Natl Acad Sci U S A (2002) 1.65

Synthesis and structure-activity relationship study of potent trypanocidal thio semicarbazone inhibitors of the trypanosomal cysteine protease cruzain. J Med Chem (2002) 1.64

Time-controlled transcardiac perfusion cross-linking for the study of protein interactions in complex tissues. Nat Biotechnol (2004) 1.63

Genes contributing to prion pathogenesis. J Gen Virol (2008) 1.51

Automatic extraction of protein point mutations using a graph bigram association. PLoS Comput Biol (2007) 1.48

Molecular phylogeny and evolution of the plant-specific seven-transmembrane MLO family. J Mol Evol (2003) 1.45

Potent inhibition of scrapie prion replication in cultured cells by bis-acridines. Proc Natl Acad Sci U S A (2003) 1.32

Cell division modulates prion accumulation in cultured cells. Proc Natl Acad Sci U S A (2007) 1.25

Directed evolution of an anti-prion protein scFv fragment to an affinity of 1 pM and its structural interpretation. J Mol Biol (2006) 1.06

Structure-activity relationship study of prion inhibition by 2-aminopyridine-3,5-dicarbonitrile-based compounds: parallel synthesis, bioactivity, and in vitro pharmacokinetics. J Med Chem (2007) 1.05

Toward the synthesis of artificial proteins: the discovery of an amphiphilic helical peptoid assembly. Chem Biol (2002) 1.05

Differences between the prion protein and its homolog Doppel: a partially structured state with implications for scrapie formation. J Mol Biol (2002) 1.04

Electron crystallography of the scrapie prion protein complexed with heavy metals. Arch Biochem Biophys (2007) 1.03

JEvTrace: refinement and variations of the evolutionary trace in JAVA. Genome Biol (2002) 0.99

Analysis of the sequence and structural features of the left-handed beta-helical fold. Proteins (2008) 0.93

Prions: so many fibers, so little infectivity. Trends Biochem Sci (2004) 0.89

Structure-activity relationship study of 9-aminoacridine compounds in scrapie-infected neuroblastoma cells. Bioorg Med Chem Lett (2006) 0.88

CoMFA and HQSAR of acylhydrazide cruzain inhibitors. Bioorg Med Chem Lett (2002) 0.87

Bis-acridines as lead antiparasitic agents: structure-activity analysis of a discrete compound library in vitro. Antimicrob Agents Chemother (2007) 0.86

Structure-activity relationships of the antimalarial agent artemisinin. 6. The development of predictive in vitro potency models using CoMFA and HQSAR methodologies. J Med Chem (2002) 0.85

Molecular modeling of the misfolded insulin subunit and amyloid fibril. Biophys J (2009) 0.83

Discriminating between cellular and misfolded prion protein by using affinity to 9-aminoacridine compounds. J Gen Virol (2007) 0.81

New local potential useful for genome annotation and 3D modeling. J Mol Biol (2003) 0.80

Site-directed mutagenesis demonstrates the plasticity of the beta helix: implications for the structure of the misfolded prion protein. Structure (2009) 0.79

Developing therapeutics for the diseases of protein misfolding. Neurology (2006) 0.77

Screening of acyl hydrazide proteinase inhibitors for antiparasitic activity against Trypanosoma brucei. Int J Antimicrob Agents (2002) 0.75