The Dundee Resource for Sequence Analysis and Structure Prediction

该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，这些工具和技术被英国和世界各地成千上万的生物科学家日常使用。该资源不仅将确保所有科学家都能随时使用这些工具，而且还将通过更好的界面和定期的面对面培训课程及其他在线材料，提高科学家和学生使用这些工具的能力。这些工具专注于蛋白质序列和结构的分析，这里简要介绍。制造植物、动物或微生物的计划被编码为DNA分子，称为其基因组。基因组可以表示为由四个不同字母（A，C，G，T）组成的长单词。病毒的基因组可能只有几千个字母，而动植物的基因组可能有几十亿个字母。基因组被分成称为基因的区域，这些区域被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20- 30，000个编码蛋白质的基因，每个蛋白质由20种不同氨基酸类型的序列组成。生物体的蛋白质序列长度从几个氨基酸到几千个氨基酸不等，可以表示为由20种不同字母类型组成的单词。蛋白质链折叠成复杂的三维形状，主要由其序列定义。蛋白质的形状，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于了解蛋白质功能至关重要。近年来，DNA测序技术取得了巨大进步，许多不同生物体的基因组已经确定。结果，现在已知了几百万种蛋白质的序列，但只有不到15万种蛋白质的详细三维结构得到了确定。构成这一资源的计算工具有助于通过对蛋白质序列进行分类和对蛋白质结构进行预测来弥合这一信息鸿沟，从而指导生物学家设计更高效和更有效的实验。该提案的一个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200个国家的科学家和我们开发的其他技术进行多达50万次预测。网站对于人类的互动是很好的，但对于计算机软件的接口就不那么有用了。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型“Web服务”接口。Web服务允许程序或应用程序从程序内部远程运行。例如，我可能有一个程序在我的台式计算机上运行，但需要在远程高性能计算机系统上进行密集计算。我们将为Web服务开发新的框架，称为“Slivka”，使Web服务的安装更容易。新资源的一个关键部分将是将许多生物的分析和预测结果存储在一个名为ProteoCache的创新数据库中。

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 150,000 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. A major objective of the proposal are to provide support, maintenance and training for the popular JPred protein structure prediction server which performs up to 500,000 predictions monthly for scientists in 200 countries and other techniques that we have developed. 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 will develop our new framework for web services called "Slivka" that makes installation of web services easier. A key part of the new resource will be to store the results of analyses and predictions for many organisms in an innovative database called the ProteoCache.