Paper Info
Title
Protein Models Comparator
Abstract
The process of 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, their ability to handle a large scale model comparison is often very limited. Most of the servers offer only a single pairwise structural comparison, and they usually do not provide a model-specific comparison with a fixed alignment between the models. 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 through outsourcing of the setup and maintenance of the hardware infrastructure. The functionality of the web application has been made available over a programmable API, so that the experiment submission and results retrieval could be automated. Protein Models Comparator is free software released on the Affero GNU Public Licence and is available at: http://www.infobiotics.org/pm-cmp This article presents a large scale model-specific protein comparison web application and provides an insight into the GAE platform and its potential value for scientific computations.
Year
Venue
Keywords
2011
Clinical Orthopaedics and Related Research
scientific computing,protein structure,protein structure prediction,model specification
Field
DocType
Volume
Data mining,Comparator,Computer science
Journal
abs/1102.4
Citations 
PageRank 
References 
0
0.34
6
Authors
2
Name
Order
Citations
PageRank
Pawel Widera1393.78
Natalio Krasnogor2121385.53