Center for Bioinformatics, Saarland Informatics Campus, Saarland University, D-66041 Saarbrücken, Germany.
J Chem Inf Model. 2021 Apr 26;61(4):1555-1559. doi: 10.1021/acs.jcim.1c00154. Epub 2021 Apr 12.
Surface pockets, cavities, and tunnels in the 3D structures of proteins play integral functional roles such as enabling enzymatic catalysis, ligand binding, or transport of ions or small molecules across biomembranes. ProPores2 facilitates understanding and analysis of these processes by identifying pores and lining residues, determining their axes, and opening closed connections via side-chain rotation. The fast stand-alone tool introduces a novel mode for pore identification, improved axis determination, and additional features such as parallel batch processing and a graphical user interface. The new web service features an integrated and customizable protein viewer with an option to analyze and view more than one structure at once. This feature facilitates side-by-side comparisons of pores in different conformations of the same protein or of identified pores before and after opening gates within the same protein. ProPores2 is freely and publicly available at https://service.bioinformatik.uni-saarland.de/propores.
蛋白质 3D 结构中的表面口袋、腔体和隧道在功能上起着重要作用，例如，能够实现酶催化、配体结合，或离子或小分子跨生物膜的运输。ProPores2 通过识别孔道和衬砌残基、确定它们的轴、通过侧链旋转打开封闭的连接，有助于理解和分析这些过程。这个快速的独立工具引入了一种新的孔道识别模式、改进的轴确定方法，以及其他功能，如并行批处理和图形用户界面。新的网络服务具有一个集成的和可定制的蛋白质查看器，用户可以一次分析和查看多个结构。这个功能方便了在同一蛋白质的不同构象或在同一蛋白质内打开门后和之前对不同孔道进行并排比较。ProPores2 可在 https://service.bioinformatik.uni-saarland.de/propores 免费公开获取。
