Domain-mediated protein interaction prediction: From genome to network (Q30010117)

21 May 2017

Domain-mediated protein interaction prediction: From genome to network (English)

1 reference

21 May 2017

1

Jüri Reimand

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Gary D. Bader

object named as

Gary D Bader

5

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author name string

Shirley Hui

2

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PubMed ID

22561014

21 May 2017

Shobhit Jain

3

1 reference

PubMed ID

22561014

21 May 2017

Brian Law

4

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PubMed ID

22561014

21 May 2017

language of work or name

English

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publication date

3 May 2012

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21 May 2017

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21 May 2017

586

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21 May 2017

2751-2763

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21 May 2017

17

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Docking and scoring protein interactions: CAPRI 2009.

21 May 2017

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Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits.

21 January 2018

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SH2 domains, interaction modules and cellular wiring

21 January 2018

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Assembly of Cell Regulatory Systems Through Protein Interaction Domains

21 January 2018

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SMART 5: domains in the context of genomes and networks

21 January 2018

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New developments in the InterPro database

21 January 2018

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The Pfam protein families database

21 January 2018

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Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins

21 January 2018

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A specificity map for the PDZ domain family

21 January 2018

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A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Protein interaction networks by proteome peptide scanning

21 January 2018

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Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides

21 January 2018

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A map of WW domain family interactions

21 January 2018

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Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis.

21 January 2018

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WW and SH3 domains, two different scaffolds to recognize proline-rich ligands

21 January 2018

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Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries

21 January 2018

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PDZ domain binding selectivity is optimized across the mouse proteome

21 January 2018

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Defining the specificity space of the human SRC homology 2 domain

21 January 2018

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Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening

21 January 2018

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DOMINO: a database of domain-peptide interactions

21 January 2018

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PDZBase: a protein-protein interaction database for PDZ-domains

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

iRefIndex: a consolidated protein interaction database with provenance

21 January 2018

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Assessing the accuracy of prediction algorithms for classification: an overview

21 January 2018

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A regularized discriminative model for the prediction of protein-peptide interactions

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

A motif-based profile scanning approach for genome-wide prediction of signaling pathways

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Using genome-wide measurements for computational prediction of SH2-peptide interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Structural basis and prediction of substrate specificity in protein serine/threonine kinases

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Predicting PDZ domain-peptide interactions from primary sequences

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

A machine learning based method for the prediction of G protein-coupled receptor-binding PDZ domain proteins

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Large-scale prediction of protein-protein interactions from structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

A physical model for PDZ-domain/peptide interactions.

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Protein structure prediction: when is it useful?

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Servers for protein structure prediction.

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Choosing negative examples for the prediction of protein-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Effect of training datasets on support vector machine prediction of protein-protein interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

The Negatome database: a reference set of non-interacting protein pairs

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1. Insights into determinants of PDZ domain specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Solution structure and backbone dynamics of the AF-6 PDZ domain/Bcr peptide complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Protein flexibility in ligand docking and virtual screening to protein kinases.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

The multiple-specificity landscape of modular peptide recognition domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Assessing semantic similarity measures for the characterization of human regulatory pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Information theory applied to the sparse gene ontology annotation network to predict novel gene function

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

A new measure for functional similarity of gene products based on Gene Ontology

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

A new method to measure the semantic similarity of GO terms

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

g:Profiler--a web server for functional interpretation of gene lists (2011 update).

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

The BioPAX community standard for pathway data sharing

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Reactome knowledgebase of human biological pathways and processes

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Relating whole-genome expression data with protein-protein interactions

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Correlation between gene expression profiles and protein-protein interactions within and across genomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

PRINCESS, a protein interaction confidence evaluation system with multiple data sources

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Ranking genes by their co-expression to subsets of pathway members.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Patterns of co-expression for protein complexes by size in Saccharomyces cerevisiae.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Deciphering the splicing code

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Predicting protein-protein interactions based only on sequences information

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Sequence-based prediction of protein-protein interactions by means of codon usage.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Predicting protein-protein interactions using signature products.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Exploiting amino acid composition for predicting protein-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Predicting protein-protein interactions in unbalanced data using the primary structure of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Network-based prediction of protein function

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Assessing experimentally derived interactions in a small world

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Gaining confidence in high-throughput protein interaction networks

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Predicting interactions in protein networks by completing defective cliques.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Extracting human protein interactions from MEDLINE using a full-sentence parser

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Overview of the BioCreative III Workshop

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Online predicted human interaction database

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

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

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

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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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

In silico two-hybrid system for the selection of physically interacting protein pairs.

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

A novel method to detect proteins evolving at correlated rates: identifying new functional relationships between coevolving proteins

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Optimization of specificity in a cellular protein interaction network by negative selection

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

A structure filter for the Eukaryotic Linear Motif Resource

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Filtering high-throughput protein-protein interaction data using a combination of genomic features

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Information assessment on predicting protein-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Probabilistic prediction and ranking of human protein-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

21 January 2018

The Protein Data Bank

1 reference

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Three-dimensional reconstruction of protein networks provides insight into human genetic disease

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

PathBLAST: a tool for alignment of protein interaction networks

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Specificity and evolvability in eukaryotic protein interaction networks

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Conserved pathways within bacteria and yeast as revealed by global protein network alignment

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Graemlin: general and robust alignment of multiple large interaction networks

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Global alignment of multiple protein interaction networks with application to functional orthology detection

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Topological network alignment uncovers biological function and phylogeny

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

21 January 2018

Biological robustness

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Disorder and sequence repeats in hub proteins and their implications for network evolution.

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

A single determinant dominates the rate of yeast protein evolution

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Relating three-dimensional structures to protein networks provides evolutionary insights

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Bringing order to protein disorder through comparative genomics and genetic interactions

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Modeling interactome: scale-free or geometric?

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Network biology: understanding the cell's functional organization

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Hierarchical organization in complex networks

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Birth and death of protein domains: a simple model of evolution explains power law behavior

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

PDZ domains and their binding partners: structure, specificity, and modification

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Signaling through scaffold, anchoring, and adaptor proteins

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Protein modules and signalling networks

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Making protein interactions druggable: targeting PDZ domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Molecular biology of human papillomavirus infection and cervical cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

A PDZ-interacting domain in CFTR is an apical membrane polarization signal

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

McKusick's Online Mendelian Inheritance in Man (OMIM)

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

SNPs, protein structure, and disease.

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Predicting the effects of amino acid substitutions on protein function

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Protein interactions in human genetic diseases.

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Modeling effects of human single nucleotide polymorphisms on protein-protein interactions

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Integrated genomic analyses of ovarian carcinoma

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

COP9 signalosome-specific phosphorylation targets p53 to degradation by the ubiquitin system

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Epidermal growth factor receptor mutations in lung cancer

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027

Probabilistic model of the human protein-protein interaction network

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.027