Enhancing the Phyre protein modelling resource: prediction of ligand binding and the impact of missense variants

蛋白质是生命的机器。蛋白质是一个长链的组分（氨基酸残基）-它的序列。基因组计划正在确定包括植物、动物和微生物在内的许多物种的蛋白质序列。实验方法揭示了蛋白质的三维结构，这些信息是生物学理解的核心，对这些知识的利用对农业、动物福利、健康和生物技术的改进具有重要意义。但这些信息往往无法从实验中获得。生物学家需要计算方法来预测蛋白质结构。帝国研究小组开发了一种功能强大且用户友好的资源，用于预测蛋白质序列的3D结构- Phyre。Phyre是由web服务器传播的——用户将感兴趣的序列粘贴到一个方框中，服务器返回预测的3D结构。事实证明，Phyre非常受欢迎，有超过4M的序列提交和超过11,000的文献引用。最近我们收到了2000多封需求信，其中150多封来自英国。2018年，我们购买了一份许可证，使我们能够将Phyre开放用于商业用途。包括人类在内的所有生物体的基因组都受到遗传密码的微小变化的影响，其中一些变化导致一种氨基酸变为另一种氨基酸，称为错义变体。有时，错义变异会损害蛋白质的生物学功能，从而导致人类和动物患病，影响作物，并改变细菌和病毒的致病性。此外，错义变异的鉴定可以用于基础研究，以揭示生物学功能。我们最近推出了一个资源Missense3D，它提供了一份关于错义变异对蛋白质结构影响的报告，并被证明在高质量的实验结构和phyre预测模型上都能产生相当的准确性。通常，蛋白质会结合一种被称为配体的小分子。了解配体在蛋白质中的结合位置对于提示蛋白质功能，确定药物可能结合的蛋白质位置以及错义变体的影响具有重要意义。在这笔拨款中，Phyre将扩展到预测配体结合位点。该方法将基于在实验确定的结构（PDB）中确定合适的模型。与目前预测配体结合位点的程序相比，一个关键的进步是使用ChEBI资源，该资源将蛋白质序列数据库（UniProt）中有关实际生物配体的信息与PDB中报告的配体联系起来。这样就可以识别出真正的配体，而不是在不同的位置返回一组可能的配体。phyre预测结构中的配体结构将使用广泛使用的将小分子对接到蛋白质中的程序（AutoDock Vina）来改进。该资助的下一步是利用预测的配体结合位点，通过第二代程序Missense3D-v2来增强对错义变异影响的预测。该方法将考虑错义变体在不同序列中是否高度保守，这表明了功能或结构的重要性，以及残基是否靠近配体结合位点。配体结合位点预测器和Missense3D-v2将以web服务器和批处理模式集成到Phyre中。此外，在这笔赠款中，我们将继续通过电子邮件帮助台和培训研讨会为用户提供支持。代码将在GitHub上发布，供社区为其开发做出贡献。

Proteins are the machinery of life. A protein is a long chain of components (amino acid residues) - its sequence. Genome projects are determining the sequences of proteins from many species including plants, animals and microbes. Experimental methods reveal the 3D structure of a protein, and this information is central to biological understanding and the exploitation of this knowledge has implications for improvements in agriculture, animal welfare, health, and biotechnology. But often this information is not available from experiment. Biologists then require computational methods to predict protein structure.The Imperial group has developed a powerful and user-friendly resource for predicting the 3D structure of a protein from its sequence - Phyre. Phyre is disseminated by a web server - a user pastes a sequence of interest into a box and the server returns the predicted 3D structure. Phyre has proved exceptionally popular with over 4M sequence submissions and over 11,000 literature citations. Recently we obtained over 2,000 letters of demand, including over 150 from the UK. In 2018, we purchased a licence that enabled us to open Phyre for commercial use. The genome of all organisms including humans are subject to small changes in the genetic code and some of these changes result in a change of one amino acid into another, known as a missense variant. Sometimes a missense variant can impair the biological function of the protein and this leads to disease in humans and animals, affect crops and alter the pathogenicity of bacteria and viruses. In addition, identification of missense variants can be used in fundamental research to unravel biological function. We have recently launched a resource Missense3D that provides a report of the effect of a missense variant on protein structure and is shown to yield comparable accuracy on both high-quality experimental structures and Phyre-predicted models. Often proteins bind a small molecule known as a ligand. Knowledge of where in the protein a ligand binds is of major benefit in terms of suggesting protein function, identifying where is a protein a drug might bind and, central to this application, the effect of a missense variant. In this grant Phyre will be extended to predict ligand binding sites. The approach will be based on identifying a suitable model within experimentally determined structures (the PDB). A key advance over current programs that predict ligand binding sites is to use a resource ChEBI that links information in the database of protein sequences (UniProt) about the actual biological ligand to ligands reported in the PDB. Thus instead of returning a set of possible ligands in different sites, the true ligand will be identified. The structure of the ligand in the Phyre-predicted structure will be refined using a widely-used program for docking small molecules into proteins (AutoDock Vina). The next step of the grant is to use the predicted ligand binding site to enhance the prediction of the impact of a missense variant via a second generation program Missense3D-v2. The approach will consider if the missense variant is highly conserved in different sequences, which indicates functional or structural importance, together with whether the residue is close to the ligand binding site. The ligand binding site predictor and Missense3D-v2 will be integrated into Phyre both in the web server and in the batch mode.In addition, in this grant we will continue to support users via an e-mail help desk and training workshops. The code will be disseminated on GitHub for the community to contribute to its development.