Welcome to Viral Post-translational Modification Database...


Introduction

VPTMdb is a comprehensive database for viruses and hosts post-translational modification sites. We have collected 1240 viral PTM sites, which integrated 818 experimental-confirmed PTM sites manually extracted from 150 publications and 422 PTMs extracted from UniProtKB/Swiss-Prot. We collected 13650 PTM sites of infected-cells. VPTMpre, a novel feature-based predictor was developed for users to predict phosphorylation sites of interests.

Statistics

The statistics of PTM sites in VPTMdb show that among eight PTM types, phosphorylation sites account for the most (692 sites) at more than 50% of the total database. The top five viruses in the number of modification sites are HHV-1(291 sites), HIV-1(180 sites), HCMV(132 sites), SARS-CoV-2(66 sites) and HAdV-2(62 sites)

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What can VPTMdb provide?

1. Friendly interface and detailed viruses and its hosts PTM information for users

2. Integrating a novel feature-based classifier for predicting viral protein phosphorylation site

3. Providing virus-human protein-protein interactions data and network visualization

2020.06.16.VPTMdb regularly updates PTM data of SARS-CoV-2!






Browse VPTMdb by viruses






Viral PTM Data



Host PTM Data



Virus-Host PPI Network

Search by sequence or protein IDs

Search by Protein Sequence(In FASTA format)

Search by Protein IDs



VPTMpre Prediction Guidelines

1. Please input your protein sequences in fasta format
2. Maximum 50 sequences for each submission
3. We provide three models to predict PTM, users choose one of them(SVM, Random Forests, Naive Bayes)
4. Because of data sets limited, now we only offer phosphorylated sites prediction, we wish to provide more types of PTMs in the future

Prediction Results

Download Prediction Results

Database Construction and Data Source

VPTMdb includes 818 experimentally verified and 422 Swiss-Prot viral PTM sites

VPTMdb also collected 13650 host PTM sites

(PS. The counting of PTM sites only considers the protein and its corresponding PTM sites, excluding the duplication caused by the type of modification)

The PTM data(includes SARS-CoV2) are organized as a 14 column table:

  • Uniprot ID, note: few proteins may not have uniprot id
  • PTM source: Experimentally verified or extracted from SwissProt
  • Post-translational modification types
  • Amino-acids position
  • Virus Name
  • Protein name
  • Gene name
  • Kinase
  • Summary: a description of the PTM site from the published study
  • PubMed ID
  • Window seq: Seven amino acid residues upstream and downstream of the modification site
  • Sequence of the PTM protein
  • Detailed virus information(strain)
  • Glycan information of viral glycosylation sites

    • Download Viral PTM data

    The Host PTM data are organized as a 12 column table:

    13650 experimentally verified host cell PTM sites

  • Uniprot ID
  • Post-translational modification types
  • Amino-acids position
  • Virus Name
  • Host name
  • Protein name
  • Gene name
  • Pubmed ID
  • Window seq: Seven amino acid residues upstream and downstream of the modification site
  • Sequence of the PTM protein
  • virus_info: virus used in the literature
  • Cell: The host cell used in the literature

    • Download Host PTM data
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