The Dundee Resource for Sequence Analysis and Structure Prediction

这一资源应用程序专注于支持和维护邓迪大学开发的计算机工具和技术，英国和世界各地的数千名生物科学家每天都在使用这些工具和技术。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以及定期面对面的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。这些工具侧重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DNA分子，并被称为其基因组。基因组可以表示为一个由四个不同字母(A、C、G、T)组成的长词。对于病毒来说，基因组可能只有几千个字母长，对于动植物来说，基因组可能长达数十亿个字母。基因组被分成称为基因的区域，这些区域由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种不同类型的氨基酸组成的序列连接在一起。来自生物体的蛋白质序列的长度从几个氨基酸到几千个氨基酸不等，可以用一个由20种不同字母类型组成的单词来表示。蛋白质链折叠成一个复杂的三维形状，主要由它的序列定义。蛋白质的形状，它的“构象”，决定了蛋白质的生物功能，所以了解蛋白质的构象对于理解蛋白质的功能至关重要。近年来，DNA测序技术取得了巨大的进步，因此已经确定了许多不同生物的基因组。因此，数百万种蛋白质的序列现在是已知的，但只有不到15万种蛋白质的详细三维结构得到了解决。构成这一资源的计算工具通过对蛋白质序列进行分类并对蛋白质结构进行预测来帮助弥合这一信息鸿沟，从而指导生物学家设计更有效和更有效的实验。该提案的一个主要目标是为广受欢迎的JPred蛋白质结构预测服务器以及我们开发的其他技术提供支持、维护和培训，该服务器每月为200个国家的科学家进行多达500,000次预测。网站对人类来说很好用，但对计算机软件来说就没那么有用了。由于我们的工具对可能对数千种蛋白质进行的大型分析很有用，因此新的资源还将支持工具的一个新颖的“网络服务”界面。Web服务允许从程序内远程运行程序或应用程序。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服务开发名为“Slivka”的新框架，使Web服务的安装变得更容易。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.