Numerous computational methods, including evolutionary-based, energy-based, and geometrical-based methods, are utilized to identify cavities inside proteins. Cavity information aids protein function annotation, drug design, poly-pharmacology, and allosteric site investigation. This article introduces “flow transfer algorithm” for rapid and effective identification of diverse protein cavities through multidimensional cavity scan. Initially, it identifies delimiter and susceptible tetrahedra to establish boundary regions and provide seed tetrahedra. Seed tetrahedron faces are precisely scanned using the maximum circle radius to transfer seed flow to neighboring tetrahedra. Seed flow continues until terminated by boundaries or forbidden faces, where a face is forbidden if the estimated maximum circle radius is less or equal to the user-defined maximum circle radius. After a seed scanning, tetrahedra involved in the flow are clustered to locate the cavity. The CRAFT web interface integrates this algorithm for protein cavity identification with enhanced user control. It supports proteins with cofactors, hydrogens, and ligands and provides comprehensive features such as 3D visualization, cavity physicochemical properties, percentage contribution graphs, and highlighted residues for each cavity. CRAFT can be accessed through its web interface at http://pitools.niper.ac.in/CRAFT , complemented by the command version available at https://github.com/PGlab-NIPER/CRAFT/ . Scientific contribution: Flow transfer algorithm is a novel geometric approach for accurate and reliable prediction of diverse protein cavities. This algorithm employs a distinct concept involving maximum circle radius within the 3D Delaunay triangulation to address diverse van der Waals radii while existing methods overlook atom specific van der Waals radii or rely on complex weighted geometric techniques.

中文翻译：

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CRAFT：基于流传递算法的网络集成型腔预测工具

许多计算方法，包括基于进化、基于能量和基于几何的方法，被用来识别蛋白质内部的空腔。腔信息有助于蛋白质功能注释、药物设计、多药理学和变构位点研究。本文介绍了“流转移算法”，通过多维空腔扫描快速有效地识别不同的蛋白质空腔。最初，它识别定界符和敏感四面体以建立边界区域并提供种子四面体。使用最大圆半径精确扫描种子四面体面，将种子流转移到相邻的四面体。种子流持续进行，直到被边界或禁止面终止，其中如果估计的最大圆半径小于或等于用户定义的最大圆半径，则禁止面。种子扫描后，参与流动的四面体聚集在一起以定位空腔。CRAFT 网络界面集成了用于蛋白质空腔识别的算法和增强的用户控制。它支持具有辅因子、氢和配体的蛋白质，并提供全面的功能，例如 3D 可视化、空腔理化特性、百分比贡献图和每个空腔的突出显示残基。CRAFT 可以通过其 Web 界面访问 http://pitools.niper.ac.in/CRAFT ，并辅以 https://github.com/PGlab-NIPER/CRAFT/ 上提供的命令版本。科学贡献：流传输算法是一种新颖的几何方法，用于准确可靠地预测不同的蛋白质空腔。该算法采用涉及 3D Delaunay 三角剖分内的最大圆半径的独特概念来解决不同的范德华半径问​​题，而现有方法则忽略了原子特定的范德华半径或依赖于复杂的加权几何技术。