Stolte Christian, Sabir Kenneth S, Heinrich Julian, Hammang Christopher J, Schafferhans Andrea, O'Donoghue Seán I
BMC Bioinformatics. 2015;16 Suppl 11(Suppl 11):S7. doi: 10.1186/1471-2105-16-S11-S7. Epub 2015 Aug 13.
To understand the molecular mechanisms that give rise to a protein's function, biologists often need to (i) find and access all related atomic-resolution 3D structures, and (ii) map sequence-based features (e.g., domains, single-nucleotide polymorphisms, post-translational modifications) onto these structures.
To streamline these processes we recently developed Aquaria, a resource offering unprecedented access to protein structure information based on an all-against-all comparison of SwissProt and PDB sequences. In this work, we provide a requirements analysis for several frequently occuring tasks in molecular biology and describe how design choices in Aquaria meet these requirements. Finally, we show how the interface can be used to explore features of a protein and gain biologically meaningful insights in two case studies conducted by domain experts.
The user interface design of Aquaria enables biologists to gain unprecedented access to molecular structures and simplifies the generation of insight. The tasks involved in mapping sequence features onto structures can be conducted easier and faster using Aquaria.
为了理解产生蛋白质功能的分子机制，生物学家通常需要：（i）找到并获取所有相关的原子分辨率三维结构，以及（ii）将基于序列的特征（例如结构域、单核苷酸多态性、翻译后修饰）映射到这些结构上。
为了简化这些过程，我们最近开发了Aquaria，这是一种基于SwissProt和PDB序列的全对全比较，提供对蛋白质结构信息前所未有的访问的资源。在这项工作中，我们对分子生物学中几个经常出现的任务进行了需求分析，并描述了Aquaria中的设计选择如何满足这些需求。最后，我们展示了在领域专家进行的两个案例研究中，如何使用该界面来探索蛋白质的特征并获得具有生物学意义的见解。
Aquaria的用户界面设计使生物学家能够前所未有的访问分子结构，并简化了见解的生成。使用Aquaria可以更轻松、更快速地完成将序列特征映射到结构上的任务。
