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Molecular principles of human virus protein–protein interactions

https://doi.org/10.1093/bioinformatics/btu763

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Evolutionary Rate Heterogeneity in Proteins with Long Disordered Regions

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Understanding protein non-folding

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Protein sequence databases

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Genome-Scale RNAi Screen for Host Factors Required for HIV Replication

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How viruses hijack cell regulation

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Emerging pathogens: the epidemiology and evolution of species jumps

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Intrinsically unstructured proteins

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Disorder and Sequence Repeats in Hub Proteins and Their Implications for Network Evolution

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Analysis of Vaccinia Virus−Host Protein−Protein Interactions: Validations of Yeast Two-Hybrid Screenings

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An African primate lentivirus (SIVsmclosely related to HIV-2

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Genetic organization of a chimpanzee lentivirus related to HIV-1

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Error and attack tolerance of complex networks

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WW domain interactions regulate the Hippo tumor suppressor pathway

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The role of disorder in interaction networks: a structural analysis

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Hepatitis C virus infection protein network

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The challenge of emerging and re-emerging infectious diseases

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RNA interference screen for human genes associated with West Nile virus infection

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Global landscape of HIV–human protein complexes

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Viral immune modulators perturb the human molecular network by common and unique strategies

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Viral Organization of Human Proteins

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Viral evasion and subversion of pattern-recognition receptor signalling

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Intrinsically unstructured proteins and their functions

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The intrinsic disorder status of the human hepatitis C virus proteome

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Viral proteins that bridge unconnected proteins and components in the human PPI network

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Epstein–Barr virus and virus human protein interaction maps

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The identification of functional modules from the genomic association of genes

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Structural principles within the human-virus protein-protein interaction network

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A Physical Interaction Network of Dengue Virus and Human Proteins

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Viruses and Interactomes in Translation

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PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life

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Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life

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The DISOPRED server for the prediction of protein disorder

inferredcites →https://doi.org/10.1093/bioinformatics/bti011openalex-snapshot

iPfam: visualization of protein–protein interactions in PDB at domain and amino acid resolutions

inferredcites →https://doi.org/10.1093/bioinformatics/btp518openalex-snapshot

ANCHOR: web server for predicting protein binding regions in disordered proteins

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Ensembl BioMarts: a hub for data retrieval across taxonomic space

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Role of the non‐homologous DNA end joining pathway in the early steps of retroviral infection

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PAML 4: Phylogenetic Analysis by Maximum Likelihood

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Comparing Models of Evolution for Ordered and Disordered Proteins

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KEGG: Kyoto Encyclopedia of Genes and Genomes

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KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1093/nar/gki442openalex-snapshot

InterProScan: protein domains identifier

inferredcites →https://doi.org/10.1093/nar/gkm259openalex-snapshot

WoLF PSORT: protein localization predictor

inferredcites →https://doi.org/10.1093/nar/gkn739openalex-snapshot

VirusMINT: a viral protein interaction database

inferredcites →https://doi.org/10.1093/nar/gkn799openalex-snapshot

PIG--the pathogen interaction gateway

inferredcites →https://doi.org/10.1093/nar/gkn892openalex-snapshot

Human Protein Reference Database--2009 update

inferredcites →https://doi.org/10.1093/nar/gkp878openalex-snapshot

The IntAct molecular interaction database in 2010

inferredcites →https://doi.org/10.1093/nar/gkq1229openalex-snapshot

DOMINE: a comprehensive collection of known and predicted domain-domain interactions

inferredcites →https://doi.org/10.1093/nar/gkr1064openalex-snapshot

ELM--the database of eukaryotic linear motifs

inferredcites →https://doi.org/10.1093/nar/gks444openalex-snapshot

iELM--a web server to explore short linear motif-mediated interactions

inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

inferredcites →https://doi.org/10.1126/science.1116804openalex-snapshot

Herpesviral Protein Networks and Their Interaction with the Human Proteome

inferredcites →https://doi.org/10.1126/science.1163581openalex-snapshot

Tight Regulation of Unstructured Proteins: From Transcript Synthesis to Protein Degradation

inferredcites →https://doi.org/10.1126/science.286.5439.509openalex-snapshot

Emergence of Scaling in Random Networks

inferredcites →https://doi.org/10.1126/scisignal.2002515openalex-snapshot

Proteome-Wide Discovery of Evolutionary Conserved Sequences in Disordered Regions

inferredcites →https://doi.org/10.1128/jvi.00059-11openalex-snapshot

Hepatitis C Virus Stimulates the Phosphatidylinositol 4-Kinase III Alpha-Dependent Phosphatidylinositol 4-Phosphate Production That Is Essential for Its Replication

inferredcites →https://doi.org/10.1128/jvi.76.10.4679-4687.2002openalex-snapshot

Viral Late Domains

inferredcites →https://doi.org/10.1128/mcb.20.22.8526-8535.2000openalex-snapshot

Latent Membrane Protein 2A of Epstein-Barr Virus Binds WW Domain E3 Protein-Ubiquitin Ligases That Ubiquitinate B-Cell Tyrosine Kinases

inferredcites →https://doi.org/10.1146/annurev-genet-110711-155522openalex-snapshot

Rules of Engagement: Molecular Insights from Host-Virus Arms Races

inferredcites →https://doi.org/10.1146/annurev.biophys.37.032807.125924openalex-snapshot

Intrinsically Disordered Proteins in Human Diseases: Introducing the D 2 Concept

inferredcites →https://doi.org/10.1186/1742-4690-9-26openalex-snapshot

Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses

inferredcites →https://doi.org/10.1186/1752-0509-5-13openalex-snapshot

When the human viral infectome and diseasome networks collide: towards a systems biology platform for the aetiology of human diseases

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BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

inferredcites →https://doi.org/10.1186/gb-2011-12-2-r14openalex-snapshot

Bringing order to protein disorder through comparative genomics and genetic interactions

inferredcites →https://doi.org/10.1201/9781420078930openalex-snapshot

Structure and Function of Intrinsically Disordered Proteins

inferredcites →https://doi.org/10.1371/journal.pbio.0030170openalex-snapshot

A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees

inferredcites →https://doi.org/10.1371/journal.pcbi.1002746openalex-snapshot

Determining Host Metabolic Limitations on Viral Replication via Integrated Modeling and Experimental Perturbation

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Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution

inferredcites →https://doi.org/10.1371/journal.pone.0060724openalex-snapshot

Marked Variability in the Extent of Protein Disorder within and between Viral Families

inferredcites →https://doi.org/10.1371/journal.ppat.0040032openalex-snapshot

The Landscape of Human Proteins Interacting with Viruses and Other Pathogens

inferredcites →https://doi.org/10.1371/journal.ppat.1002894openalex-snapshot

The Battle over mTOR: An Emerging Theatre in Host–Pathogen Immunity

inferredcites →https://doi.org/10.1371/journal.ppat.1003778openalex-snapshot

Signatures of Pleiotropy, Economy and Convergent Evolution in a Domain-Resolved Map of Human–Virus Protein–Protein Interaction Networks

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Unfoldomics of Human Genetic Diseases: Illustrative Examples of Ordered and Intrinsically Disordered Members of the Human Diseasome

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Initiation of Lytic DNA Replication in Epstein–Barr Virus: Search for a Common Family Mechanism

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Understanding eukaryotic linear motifs and their role in cell signaling and regulation

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Toward a three-dimensional view of protein networks between species

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