Predicting protein-protein interactions in the context of protein evolution (Q37660067)

21 August 2017

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title

Predicting protein-protein interactions in the context of protein evolution (English)

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protein-protein interaction

21 August 2017

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Charlotte M Deane

3

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author name string

Anna C F Lewis

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1

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PubMed ID

20024067

21 August 2017

Ramazan Saeed

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2

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21 August 2017

28 September 2009

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21 August 2017

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21 August 2017

6

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21 August 2017

55-64

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21 August 2017

1

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High-quality binary protein interaction map of the yeast interactome network

21 August 2017

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An in vivo map of the yeast protein interactome

21 January 2018

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Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae

21 January 2018

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Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

21 January 2018

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Proteome survey reveals modularity of the yeast cell machinery

21 January 2018

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Functional organization of the yeast proteome by systematic analysis of protein complexes

21 January 2018

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Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

21 January 2018

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A comprehensive two-hybrid analysis to explore the yeast protein interactome

21 January 2018

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A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae

21 January 2018

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Pathguide: a pathway resource list

21 January 2018

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How complete are current yeast and human protein-interaction networks?

21 January 2018

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Towards an understanding of complex protein networks

21 January 2018

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Evolution at the system level: the natural history of protein interaction networks

21 January 2018

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Comparative assessment of large-scale data sets of protein-protein interactions

21 January 2018

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Protein interactions: two methods for assessment of the reliability of high throughput observations

21 January 2018

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A novel genetic system to detect protein-protein interactions

21 January 2018

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The tandem affinity purification (TAP) method: a general procedure of protein complex purification

21 January 2018

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Yeast two-hybrid, a powerful tool for systems biology

21 January 2018

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Mapping multiprotein complexes by affinity purification and mass spectrometry

21 January 2018

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Questioning the ubiquity of neofunctionalization

21 January 2018

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Increasing specificity in high-throughput yeast two-hybrid experiments

21 January 2018

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Analyzing yeast protein-protein interaction data obtained from different sources

21 January 2018

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Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets

21 January 2018

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Evolutionary rate depends on number of protein-protein interactions independently of gene expression level

21 January 2018

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A network of protein-protein interactions in yeast

21 January 2018

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Protein protein interactions, evolutionary rate, abundance and age.

21 January 2018

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Gaining confidence in high-throughput protein interaction networks

21 January 2018

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Conserved patterns of protein interaction in multiple species

21 January 2018

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An assessment of the uses of homologous interactions.

21 January 2018

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Interaction generality, a measurement to assess the reliability of a protein-protein interaction

21 January 2018

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Construction of reliable protein–protein interaction networks with a new interaction generality measure

21 January 2018

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Increasing confidence of protein interactomes using network topological metrics.

21 January 2018

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An introduction to ROC analysis

21 January 2018

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Global topological features of cancer proteins in the human interactome

21 January 2018

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CYGD: the Comprehensive Yeast Genome Database

21 January 2018

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Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

21 January 2018

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Choosing negative examples for the prediction of protein-protein interactions

21 January 2018

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An integrated view of protein evolution

21 January 2018

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Evolution and dynamics of protein interactions and networks.

21 January 2018

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The genetic theory of adaptation: a brief history

21 January 2018

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Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins

21 January 2018

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Evolutionary rate in the protein interaction network

21 January 2018

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Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks

21 January 2018

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Molecular evolution in large genetic networks: does connectivity equal constraint?

21 January 2018

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A single determinant dominates the rate of yeast protein evolution

21 January 2018

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Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?

21 January 2018

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A hot spot of binding energy in a hormone-receptor interface

21 January 2018

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Hot spots--a review of the protein-protein interface determinant amino-acid residues

21 January 2018

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Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.

21 January 2018

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Diversity of protein-protein interactions

21 January 2018

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The constraints protein-protein interactions place on sequence divergence.

21 January 2018

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Protein co-evolution, co-adaptation and interactions

21 January 2018

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Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages

21 January 2018

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Systematic discovery of analogous enzymes in thiamin biosynthesis

21 January 2018

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Use of logic relationships to decipher protein network organization

21 January 2018

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Predicting protein function by genomic context: quantitative evaluation and qualitative inferences

21 January 2018

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21 January 2018

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Structure, function, and evolution of transient and obligate protein-protein interactions

21 January 2018

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Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions

21 January 2018

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High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

21 January 2018

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The effect of sequence evolution on protein structural divergence.

21 January 2018

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Empirical and structural models for insertions and deletions in the divergent evolution of proteins.

21 January 2018

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The effect of insertions and deletions on wirings in protein-protein interaction networks: a large-scale study.

21 January 2018

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Specificity in protein interactions and its relationship with sequence diversity and coevolution

21 January 2018

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21 January 2018

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Emergence of Scaling in Random Networks

21 January 2018

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A general theory of bibliometric and other cumulative advantage processes

21 January 2018

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The Structure and Function of Complex Networks

21 January 2018

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Evolution and topology in the yeast protein interaction network

21 January 2018

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Evolution by gene duplication: an update

21 January 2018

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The 2R hypothesis: an update

21 January 2018

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Yeast genome evolution--the origin of the species

21 January 2018

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Dosage sensitivity and the evolution of gene families in yeast

21 January 2018

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Modeling protein network evolution under genome duplication and domain shuffling

21 January 2018

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Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence

21 January 2018

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Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications

21 January 2018

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Inferring network mechanisms: the Drosophila melanogaster protein interaction network

21 January 2018

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A likelihood approach to analysis of network data

21 January 2018

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Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum

21 January 2018

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Domain-oriented edge-based alignment of protein interaction networks

21 January 2018

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IsoRankN: spectral methods for global alignment of multiple protein networks

21 January 2018

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Global alignment of protein-protein interaction networks by graph matching methods

21 January 2018

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Modeling cellular machinery through biological network comparison

21 January 2018

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A statistical approach using network structure in the prediction of protein characteristics.

21 January 2018

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Hierarchical structure and the prediction of missing links in networks

21 January 2018

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Functional and topological characterization of protein interaction networks.

21 January 2018

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Detecting protein function and protein-protein interactions from genome sequences

21 January 2018

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The use of gene clusters to infer functional coupling

21 January 2018

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Protein interaction maps for complete genomes based on gene fusion events

21 January 2018

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Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

21 January 2018

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Protein interaction mapping in C. elegans using proteins involved in vulval development

21 January 2018

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Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs".

21 January 2018

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Protein-protein interactions more conserved within species than across species

21 January 2018

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Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs

21 January 2018

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Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis

21 January 2018

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Comparative interactomics: comparing apples and pears?

21 January 2018

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Co-evolution of proteins with their interaction partners

21 January 2018

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Computational methods for the prediction of protein interactions

21 January 2018

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Prediction of protein-protein interactions by docking methods.

21 January 2018

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Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking.

21 January 2018

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A structural perspective on protein-protein interactions.

21 January 2018

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Prediction of protein-protein interactions based on surface patch comparison.

21 January 2018

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Oligomeric protein structure networks: insights into protein-protein interactions

21 January 2018

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Studying noncovalent protein complexes by electrospray ionization mass spectrometry

21 January 2018

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Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures

21 January 2018

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SCOP database in 2004: refinements integrate structure and sequence family data

21 January 2018

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Pfam: clans, web tools and services

21 January 2018

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CDD: a conserved domain database for interactive domain family analysis

21 January 2018

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21 January 2018

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Inferring domain-domain interactions from protein-protein interactions

21 January 2018

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Inferring protein domain interactions from databases of interacting proteins

21 January 2018

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PROTEIN FAMILIES AND THEIR EVOLUTION—A STRUCTURAL PERSPECTIVE

21 January 2018

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Evolution of protein domain promiscuity in eukaryotes

21 January 2018

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Analysing six types of protein-protein interfaces

21 January 2018

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Bridging structural biology and genomics: assessing protein interaction data with known complexes

21 January 2018

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The Relationship Between Sequence and Interaction Divergence in Proteins

21 January 2018

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Protein interactions: is seeing believing?

21 January 2018

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21 January 2018

Identifiers

DOI

10.1039/B916371A

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21 August 2017

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PubMed ID

20024067