MOLEonline: a web-based tool for analysing channels, tunnels, and pores (2025 update).

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Bioinformatics (Oxford, England) Pub Date : 2025-09-01 DOI:10.1093/bioinformatics/btaf486

Tomáš Raček, Dušan Vel'ký, Gabriela Bučeková, Ondřej Schindler, Ivana Hutařová Vařeková, Anna Špačková, Václav Bazgier, Karel Berka, Radka Svobodová

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Abstract

Summary: MOLEonline is an interactive, web-based tool designed to detect and analyse channels (pores and tunnels) within protein structures. The latest version of MOLEonline addresses the limitations of its predecessor by integrating the Mol* viewer for visualization and offering a streamlined, fully interactive user experience. The new features include colouring tunnels in the 3D viewer based on their physicochemical properties. A 2D representation of the protein structure and calculated tunnels is generated using 2DProts. Users can now store tunnels directly in the mmCIF file format, facilitating sharing via the community-standard FAIR format for structural data. In addition, the ability to store and load computation settings ensures the reproducibility of tunnel computation results. Integration with the ChannelsDB 2.0 database allows users to access precomputed tunnels.

Availability and implementation: The MOLEonline application is freely available at https://moleonline.cz with no login requirement, its source code is stored at GitHub under the MIT licence at https://github.com/sb-ncbr/moleonline-web, and archived at Figshare at https://doi.org/10.6084/m9.figshare.29816174.

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MOLEonline：一个基于网络的分析渠道、隧道和孔隙的工具（2025年更新）。

MOLEonline是一个交互式的基于网络的工具，用于检测和分析蛋白质结构中的通道（孔隙和隧道）。最新版本的MOLEonline解决了其前身的局限性，集成了Mol*查看器的可视化，并提供了一个精简的，完全互动的用户体验。新功能包括在3D查看器中根据隧道的物理化学性质为其着色。使用2DProts生成蛋白质结构和计算隧道的二维表示。用户现在可以直接以mmCIF文件格式存储隧道，方便通过社区标准的FAIR格式共享结构数据。此外，存储和加载计算设置的能力确保了隧道计算结果的再现性。与ChannelsDB 2.0数据库集成，允许用户访问预先计算的隧道。可用性和实现：MOLEonline应用程序可在https://moleonline.cz免费获得，无需登录，其源代码存储在MIT许可下的GitHub （https://github.com/sb-ncbr/moleonline-web）中，并存档在Figshare （https://doi.org/10.6084/m9.figshare.29816174.Supplementary）中。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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