G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures

Oz Solomon, Vered Kunik, Amos Simon, Nitzan Kol, Ortal Barel, Atar Lev, Ninette Amariglio, Raz Somech, Gidi Rechavi, Eran Eyal*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Background: Evaluation of the possible implications of genomic variants is an increasingly important task in the current high throughput sequencing era. Structural information however is still not routinely exploited during this evaluation process. The main reasons can be attributed to the partial structural coverage of the human proteome and the lack of tools which conveniently convert genomic positions, which are the frequent output of genomic pipelines, to proteins and structure coordinates. Results: We present G23D, a tool for conversion of human genomic coordinates to protein coordinates and protein structures. G23D allows mapping of genomic positions/variants on evolutionary related (and not only identical) protein three dimensional (3D) structures as well as on theoretical models. By doing so it significantly extends the space of variants for which structural insight is feasible. To facilitate interpretation of the variant consequence, pathogenic variants, functional sites and polymorphism sites are displayed on protein sequence and structure diagrams alongside the input variants. G23D also provides modeling of the mutant structure, analysis of intra-protein contacts and instant access to functional predictions and predictions of thermo-stability changes. G23D is available at http://www.sheba-cancer.org.il/G23D. Conclusions: G23D extends the fraction of variants for which structural analysis is applicable and provides better and faster accessibility for structural data to biologists and geneticists who routinely work with genomic information.

Original languageEnglish
Article number681
JournalBMC Genomics
Volume17
Issue number1
DOIs
StatePublished - 26 Aug 2016

Keywords

  • Mutation
  • Protein
  • Structure
  • Variant
  • Visualization

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