The Dundee Resource for Protein Structure Prediction and Sequence Analysis

这个资源应用程序的重点是支持和维护邓迪大学开发的计算机工具和技术，这些工具和技术每天都被英国和世界各地成千上万的生物科学家使用。该资源不仅将确保所有科学家都能随时获得这些工具，而且还将通过更好的界面和定期的面对面培训课程和其他在线材料提高科学家和学生使用这些工具的能力。这些工具主要用于蛋白质序列和结构的分析，这里简要介绍一下。制造植物、动物或微生物的计划被编码为分子DNA，称为其基因组。基因组可以被表示成一个由四个不同字母（a， C， G， T）组成的长单词。病毒的基因组可能有几千个字母长，而植物和动物的基因组可能有几十亿个字母长。基因组被分成称为基因的区域，这些区域通过复杂的分子机器翻译成其他分子，如蛋白质。人类和其他动物有2 -3万个编码蛋白质的基因，每种蛋白质由20种不同的氨基酸类型连接成一条链组成。一个生物体的蛋白质序列的长度从几个氨基酸到几千个不等，可以用20个不同字母类型组成的一个单词来表示。蛋白质链折叠成复杂的三维形状，主要由其序列决定。蛋白质的形状，即它的“构象”，决定了蛋白质的生物学功能，因此了解蛋白质的构象对了解蛋白质的功能至关重要。近年来，DNA测序技术取得了巨大进步，因此许多不同生物体的基因组已经确定。其结果是，现在已经知道了几百万种蛋白质的序列，但只有不到10万种蛋白质的详细三维结构被计算出来。计算工具将弥补这一资源，通过对蛋白质序列进行分类和对蛋白质结构进行预测，帮助生物学家设计更高效和有效的实验，从而弥合这一信息鸿沟。该提案的主要目标是为流行的JPred蛋白质结构预测服务器提供支持，维护和培训，该服务器每月为140个国家的科学家进行多达95,000次预测，TarO蛋白质序列分析套件和Kinomer蛋白激酶分类器和数据库。新的资源将这些独立的工具与一个一致的外观和感觉集成在一起，使研究人员和工具开发人员能够以一种超越传统网站的新方式使用它们。网站很适合人类与之交互，但对于计算机软件来说，与之交互就不那么有用了。由于我们的工具对于可能对数千种蛋白质进行的大型分析非常有用，因此新资源还将支持工具的新颖“web服务”接口。Web服务允许从程序内部远程运行程序或应用程序。例如，我可能在我的台式计算机上运行一个程序，但需要在远程高性能计算机系统上进行密集计算。我们最近开发了一种部署web服务的新方法（称为JABAWS），它使web服务的安装更加简单。新资源的一个关键部分是将更复杂的应用程序（如结构预测）添加到Jabaws中，从而使程序员和最终用户可以随时使用它们

This resource application is focused on supporting and maintaining computer tools and techniques developed at the University of Dundee that are in daily use by thousands of biological scientists throughout the UK and the world. The resource will not only ensure that these tools are readily available to all scientists, but also improve the ability of scientists and students to use them through better interfaces and via regular face-to-face training courses and other on-line materials. The tools focus on the analysis of protein sequences and structures which are briefly introduced here. The plans to make a plant, animal or micro-organism are encoded as the molecule DNA and known as its genome. The genome can be represented as a long word made up of four different letters (A, C, G, T). The genome may be a few thousand letters long for a virus, to several billion letters for plants and animals. The genome is divided up into regions called genes which are translated by complex molecular machines into other molecules such as proteins. Humans and other animals have 20-30,000 genes that code for proteins and each protein made up of a sequence of 20 different amino acid types joined together in a chain. Protein sequences from an organism vary in length from a few amino acids, to several thousand and can be represented as a word made up of 20 different letter types. The protein chain folds up into a complex three-dimensional shape that is defined primarily by its sequence. The shape of the protein, its "conformation", dictates the biological function of the protein, so understanding the conformation of a protein is vitally important to understanding the protein function. Over recent years there have been huge advances in technology to sequence DNA and so the genomes of many different organisms have been determined. As a consequence, the sequences of several million proteins are now known but less than 100,000 have had their detailed three-dimensional structures worked out. The computational tools that will make up this resource help to bridge this information gap by classifying protein sequences and making predictions of protein structure that can guide biologists to design more efficient and effective experiments. The main objectives of the proposal are to provide support, maintenance and training for the popular JPred protein structure prediction server which performs up to 95,000 predictions monthly for scientists in 140 countries, the TarO protein sequence analysis suite and Kinomer protein kinase classifier and database. The new resource will integrate these individual tools with a consistent look-and-feel and make them available to researchers and tool developers in new ways over and above a conventional web site. Web sites are good for humans to interact with, but less useful for computer software to interface to. Since our tools are useful for large analyses that might be done on many thousands of proteins, the new resource will also support a novel "web services" interface to the tools. Web services allow a program or application to be run remotely from within a program. For example, I might have a program running on my desktop computer, but call for an intensive calculation to be done on a remote high-performance computer system. We have recently developed a new method to deploy web services (called JABAWS) that makes installation of web services straightforward. A key part of the new resource will be to add more complex applications such as structure prediction to Jabaws and so make them readily available to programmers and end-users