Protein Models Comparator

Protein Models Comparator (pm-cmp) is a scalable web application for a fast distributed comparison of protein models (3D protein structures based on the same sequence of amino acids) with a number of measures (currently RMSD, GDT TS, TM-score and Q-score). It can be used to evaluate structural models against a target (e.g. the native structure) or to compare the models against each other (e.g. for further analysis with clustering algorithms).

It runs on the Google App Engine cloud platform and is a showcase of how the emerging PaaS (Platform as a Service) technology could be used to simplify the development of scalable bioinformatics services.

The functionality of pm-cmp is accessible through API which allows a full automation of the experiment submission and results retrieval (example Python script is provided). Pm-cmp is a free software released under the Affero GNU Public Licence and its source code is available for download.

Publications

• URL eprint code BibTeX
  P. Widera, N. Krasnogor
  Protein Models Comparator: Scalable Bioinformatics Computing on the Google App Engine Platform
  in Computing Research Repository, arXiv:1102.4293v2, February 2011

  @ARTICLE{Widera2011,
    title = {Protein Models Comparator: Scalable Bioinformatics Computing on the Google App Engine Platform},
    author = {Widera, Paweł and Krasnogor, Natalio},
    year = 2011,
    url = {http://arxiv.org/abs/1102.4293},
    month = feb,
    journal = {Computing Research Repository},
    volume = {arXiv:1102.4293v2}