DREAMM：一个基于网络的药物设计服务器，用于靶向药物设计的新工作流程，以药物蛋白质-膜界面。
DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design.
机构信息
Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece.
Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Athens 15784, Greece.
出版信息
Bioinformatics. 2022 Dec 13;38(24):5449-5451. doi: 10.1093/bioinformatics/btac680.
SUMMARY
The allosteric modulation of peripheral membrane proteins (PMPs) by targeting protein-membrane interactions with drug-like molecules represents a new promising therapeutic strategy for proteins currently considered undruggable. However, the accessibility of protein-membrane interfaces by small molecules has been so far unexplored, possibly due to the complexity of the interface, the limited protein-membrane structural information and the lack of computational workflows to study it. Herein, we present a pipeline for drugging protein-membrane interfaces using the DREAMM (Drugging pRotein mEmbrAne Machine learning Method) web server. DREAMM works in the back end with a fast and robust ensemble machine learning algorithm for identifying protein-membrane interfaces of PMPs. Additionally, DREAMM also identifies binding pockets in the vicinity of the predicted membrane-penetrating amino acids in protein conformational ensembles provided by the user or generated within DREAMM.
AVAILABILITY AND IMPLEMENTATION
DREAMM web server is accessible via https://dreamm.ni4os.eu.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
通过靶向蛋白-膜相互作用的药物样分子来调节外周膜蛋白（PMPs）的变构，为目前认为不可成药的蛋白提供了一种新的有前途的治疗策略。然而，小分子与蛋白-膜界面的可及性迄今仍未得到探索，这可能是由于界面的复杂性、有限的蛋白-膜结构信息以及缺乏用于研究它的计算工作流程。在此，我们提出了一个使用 DREAMM（Drugging pRotein mEmbrAne Machine learning Method）网络服务器对蛋白-膜界面进行药物设计的管道。DREAMM 在后端使用快速而强大的集成机器学习算法来识别 PMP 的蛋白-膜界面。此外，DREAMM 还可以在用户提供或在 DREAMM 内部生成的蛋白构象集合中预测的穿膜氨基酸附近识别结合口袋。
可用性和实现
DREAMM 网络服务器可通过 https://dreamm.ni4os.eu 访问。
补充信息
补充数据可在“Bioinformatics”在线获取。
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