Dataset Information

VPDB: Viral Protein Structural Database.

ABSTRACT:

Unlabelled

Viral Protein Database is an interactive database for three dimensional viral proteins. Our aim is to provide a comprehensive resource to the community of structural virology, with an emphasis on the description of derived data from structural biology. Currently, VPDB includes ˜1,670 viral protein structures from >277 viruses with more than 465 virus strains. The whole database can be easily accessed through the user convenience text search. Interactivity has been enhanced by using Jmol, WebMol and Strap to visualize the viral protein molecular structure.

Availability

The database is available for free at http://www.vpdb.bicpu.edu.in.

SUBMITTER: Sharma OP

PROVIDER: S-EPMC3134783 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

VPDB: Viral Protein Structural Database.

Sharma Om Prakash OP Jadhav Ankush A Hussain Afzal A Kumar Muthuvel Suresh MS

Bioinformation 20110706 8

<h4>Unlabelled</h4>Viral Protein Database is an interactive database for three dimensional viral proteins. Our aim is to provide a comprehensive resource to the community of structural virology, with an emphasis on the description of derived data from structural biology. Currently, VPDB includes ˜1,670 viral protein structures from >277 viruses with more than 465 virus strains. The whole database can be easily accessed through the user convenience text search. Interactivity has been enhanced by ...[more]

PMID: 21769196

Similar Datasets

Project description:MotivationViruses infect, reprogram, and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases.ResultsHere we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240,311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from "conservative" to "eXtremely Conservative" resulted in 37,841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ∼24% on average (up to ∼42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.AvailabilityThe resources are available on the iVirus platform at (doi.org/10.25739/9vze-4143).Supplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

VPDB: Viral Protein Structural Database.

Unlabelled

Availability

Publications

VPDB: Viral Protein Structural Database.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets