Insilichem, Department of chemistry, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain.
Bioinformatics. 2023 Aug 1;39(8). doi: 10.1093/bioinformatics/btad476.
Graphical analysis of the molecular structure of proteins can be very complex. Full-atom representations retain most geometric information but are generally crowded, and key structural patterns can be challenging to identify. Non-full-atom representations could be more instructive on physicochemical aspects but be insufficiently detailed regarding shapes (e.g. entity beans-like models in coarse grain approaches) or simple properties of amino acids (e.g. representation of superficial electrostatic properties). In this work, we present TALAIA a visual dictionary that aims to provide another layer of structural representations.TALAIA offers a visual grammar that combines simple representations of amino acids while retaining their general geometry and physicochemical properties. It uses unique objects, with differentiated shapes and colors to represent amino acids. It makes easier to spot crucial molecular information, including patches of amino acids or key interactions between side chains. Most conventions used in TALAIA are standard in chemistry and biochemistry, so experimentalists and modelers can rapidly grasp the meaning of any TALAIA depiction.
We propose TALAIA as a tool that renders protein structures and encodes structure and physicochemical aspects as a simple visual grammar. The approach is fast, highly informative, and intuitive, allowing the identification of possible interactions, hydrophobic patches, and other characteristic structural features at first glance. The first implementation of TALAIA can be found at https://github.com/insilichem/talaia.
蛋白质分子结构的图形分析可能非常复杂。全原子表示保留了大多数几何信息，但通常比较拥挤，并且关键的结构模式可能难以识别。非全原子表示在物理化学方面可能更具说明性，但在形状方面（例如粗粒度方法中的实体 bean 样模型）或氨基酸的简单性质（例如表面静电性质的表示）可能不够详细。在这项工作中，我们提出了 TALAIA，这是一个视觉字典，旨在提供另一层结构表示。TALAIA 提供了一种视觉语法，它结合了氨基酸的简单表示，同时保留了它们的一般几何形状和物理化学性质。它使用独特的对象，具有不同的形状和颜色来表示氨基酸。它使人们更容易发现关键的分子信息，包括氨基酸补丁或侧链之间的关键相互作用。TALAIA 中使用的大多数约定在化学和生物化学中都是标准的，因此实验家和建模者可以快速理解任何 TALAIA 表示的含义。
我们提出 TALAIA 作为一种工具，它可以呈现蛋白质结构，并将结构和物理化学方面编码为简单的视觉语法。该方法快速、信息量丰富且直观，允许一眼就能识别可能的相互作用、疏水区和其他特征结构特征。TALAIA 的第一个实现可以在 https://github.com/insilichem/talaia 上找到。
