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: URL 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 .
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: URL 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 .
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process of
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template free
template-free
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their ability to handle a
they are not well suited for
R
is often very limited. Most of the servers
: (1) they operate with methods designed to compare actual proteins, not the models of the same protein, (2) majority of them
R
, and they usually do not provide a model-specific comparison with a fixed alignment between the models
and are unable to scale up to a required order of thousands of comparisons
D
through outsourcing of the setup and maintenance of the hardware infrastructure
R
the web application has been made available over a programmable API , so that
pm-cmp is accessible through API which allows a full automation of
D
could be automated
A
with its source code
R
large scale
new web application addressing the need for a large-scale
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comparison web application
structure comparison
A
(Google App Engine)
R
potential value for scientific computations
usefulness in scientific computing