Protein Models Comparator：Google App Engine平台上的可扩展生物信息学计算
Protein Models Comparator: Scalable Bioinformatics Computing on the Google App Engine Platform
摘要：
计算机生成的蛋白质结构模型之间的比较是蛋白质结构预测的重要组成部分。它有许多用途，包括模型质量评估，从大量候选模型中选择最终模型，或优化无模板建模和细化中使用的能量函数参数。虽然许多蛋白质比较方法可以在许多网络服务器上在线获得，但它们并不适合大规模模型比较：（1）它们使用旨在比较实际蛋白质的方法，而不是同一蛋白质的模型，（2）它们中的大多数只提供单个成对结构比较，并且无法扩展到所需的数千次比较。为了弥合蛋白质和模型结构比较之间的差距，我们开发了蛋白质模型比较器（pm-cmp）。为了能够按需提供可扩展性并处理大型比较实验，pm-cmp是在“云中”实现的。Protein Models Comparator是一个可扩展的Web应用程序，用于快速比较蛋白质模型与RMSD，GDT TS，TM评分和Q评分测量。它运行在Google App Engine（GAE）云平台上，展示了如何使用新兴的PaaS（平台即服务）技术来简化可扩展生物信息学服务的开发。pm-cmp的功能可通过API访问，该API允许实验提交和结果检索的完全自动化。Protein Models Comparator是在Affero GNU公共许可证上发布的免费软件，其源代码可在以下网址获得：http://www.infobiotics.org/pm-cmp本文介绍了一个新的Web应用程序，该应用程序解决了大规模模型特定蛋白质结构比较的需求，并深入了解了GAE（Google App Engine）平台及其在科学计算中的实用性。
英文摘要：
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.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
