Structures and files for MD simulations of ternary complexes FKBP12-FRAP-rapamycin and FKBP12-CEP250-WDB002

The directory contains the structures and files used to start molecular dynamics simulations of apo and holo forms of the ternary complexes FKBP12-FRAP-rapamycin and FKBP12-CEP250-WDB002 as well as the binary complexes: FKBP12-rapamycin, FRAP-rapamycin, FKBP12-WDB002 and CEP250-WDB002. The files required to calculate the MM/GBSA binding free energies and frequency of occurrence of water-mediated hydrogen bonds between protein chains are also included. Details about the modeling and simulations can be found in the paper: Molecular glues stabilize water-mediated hydrogen bonds in ternary complexes-Apoorva Mathur, Mariona Alegre Canela, Max von Graevenitz, Chiara Gerstner, Ariane Nunes-Alves*本目录包含用于启动FKBP12-FRAP-雷帕霉素、FKBP12-CEP250-WDB002两种三元复合物，以及FKBP12-雷帕霉素、FRAP-雷帕霉素、FKBP12-WDB002、CEP250-WDB002四种二元复合物的脱辅基态（apo form）与全配体态（holo form）的分子动力学模拟（molecular dynamics simulations）所需的结构与文件。同时还包含用于计算分子力学/广义玻恩表面积法（MM/GBSA）结合自由能，以及蛋白链间水介导氢键（water-mediated hydrogen bonds）出现频率所需的相关文件。 有关建模与模拟的详细信息可参阅以下论文： 《分子胶可稳定三元复合物中的水介导氢键》——Apoorva Mathur、Mariona Alegre Canela、Max von Graevenitz、Chiara Gerstner、Ariane Nunes-Alves*