Department of Cell and Molecular Biology, Uppsala University, BMC - Box 596, Uppsala, SE 751 24, Sweden.
Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands.
Bioinformatics. 2024 Nov 1;40(11). doi: 10.1093/bioinformatics/btae662.
Memprot.GPCR-ModSim leverages our previous web-based protocol, which was limited to class-A G protein-coupled receptors, to become the first one-stop web server for the modelling and simulation of any membrane protein system. Motivated by the exponential growth of experimental structures and the breakthrough of deep-learning-based structural modelling, the server accepts as input either a membrane-protein sequence, in which case it reports the associated AlphaFold model, or a 3D (experimental, modelled) structure, including quaternary complexes with associated proteins and/or ligands of any kind. In both cases, the molecular dynamics (MD) protocol produces a membrane-embedded, solvated, and equilibrated system, ready to be used as a starting point for further MD simulations, including ligand-binding free energy calculations.
Memprot.GPCR-ModSim web server is publicly available at https://memprot.gpcr-modsim.org/. The standalone modules for 3D modelling (PyModSim) or membrane embedding and MD equilibration (PyMemDyn) are available under CC BY-NC 4.0 license terms at the GitHub repository https://github.com/GPCR-ModSim/.
Memprot.GPCR-ModSim 利用我们之前的基于网络的协议，该协议仅限于 A 类 G 蛋白偶联受体，成为第一个用于任何膜蛋白系统建模和模拟的一站式网络服务器。受实验结构的指数级增长和基于深度学习的结构建模的突破的推动，该服务器接受输入为膜蛋白序列，在这种情况下，它会报告相关的 AlphaFold 模型，或者是 3D（实验、建模）结构，包括与任何类型的相关蛋白质和/或配体的四级复合物。在这两种情况下，分子动力学（MD）协议都会产生一个嵌入式、溶剂化和平衡的系统，可作为进一步 MD 模拟的起点，包括配体结合自由能计算。
Memprot.GPCR-ModSim 网络服务器可在 https://memprot.gpcr-modsim.org/ 上公开访问。用于 3D 建模（PyModSim）或膜嵌入和 MD 平衡（PyMemDyn）的独立模块可根据 CC BY-NC 4.0 许可证条款在 GitHub 存储库 https://github.com/GPCR-ModSim/ 上获得。
