The Dundee Resource for Sequence Analysis and Structure Prediction (DRSASP) - 2023 and Beyond

这一资源应用程序的重点是继续支持邓迪大学开发的计算机工具和技术，英国和世界各地数以千计的生物研究科学家和学生每天都在使用这些工具和技术。该资源不仅将确保所有人都可以随时使用这些工具，而且还将通过更好的界面以及通过培训视频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。组成这一资源的计算工具将通过对蛋白质序列进行分类并以易于解释的方式预测蛋白质结构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。这项提议将为广受欢迎的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。JPred蛋白质结构预测服务器每月为100个国家的科学家执行约30,000次预测。它将增强JPred，包括预测蛋白质三维结构的最新方法的结构预测。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，该资源还支持使用Dundee开发的名为“Slivka”的技术的工具的新颖“Web服务”接口，这使得添加新服务变得容易。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。我们的服务是复杂的计算机系统，但我们将使用称为Docker和Conda的技术来将它们打包，其他机构可以安装和运行它们。这将有助于确保即使Dundee的服务失败，服务仍可用。

This resource application is focused continuing to support computer tools and techniques developed at the University of Dundee that are in daily use by thousands of biological research scientists and students throughout the UK and the world. The resource will not only ensure that these tools are readily available to all, but also improve the ability of scientists and students to use them through better interfaces and via training videos 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 available in easy to interpret way that can guide biologists to design more efficient and effective experiments. This proposal will provide support, maintenance and training for the popular JPred protein structure prediction server which performs around 30,000 predictions monthly for scientists in >100 countries and other techniques that we have developed. It will enhance JPred to include structure predictions from the latest methods to predict protein three-dimensional structures. 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 resource also supports a novel "web services" interface to the tools using technology called 'Slivka' developed in Dundee that makes it easy to add new services. 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. Our services are complex computer systems but we will use technologies called docker and conda to package them in a way that other institutions can install and run them. This will help ensure the services remain available even if those at Dundee fail.