Protein Models Comparator: Scalable Bioinformatics Computing on the Google App Engine Platform

The comparison of computer generated protein structural models is an important element of protein structure prediction. It has many uses including model quality evaluation, selection of the final models from a large set of candidates or optimisation of parameters of energy functions used in template-free modelling and refinement. Although many protein comparison methods are available online on numerous web servers, they are not well suited for large scale model comparison: (1) they operate with methods designed to compare actual proteins, not the models of the same protein, (2) majority of them offer only a single pairwise structural comparison and are unable to scale up to a required order of thousands of comparisons. To bridge the gap between the protein and model structure comparison we have developed the Protein Models Comparator (pm-cmp). To be able to deliver the scalability on demand and handle large comparison experiments the pm-cmp was implemented "in the cloud". Protein Models Comparator is a scalable web application for a fast distributed comparison of protein models with RMSD, GDT TS, TM-score and Q-score measures. It runs on the Google App Engine (GAE) 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. Protein Models Comparator is free software released on the Affero GNU Public Licence and is available with its source code at: http://www.infobiotics.org/pm-cmp This article presents a new web application addressing the need for a large-scale model-specific protein structure comparison and provides an insight into the GAE (Google App Engine) platform and its usefulness in scientific computing.