通过RCSB Protein Data Bank数据库(https://www.rcsb.org/)查找Caspase-1/GSDMD/NRP3蛋白的晶体结构,筛选条件物种设置为人类,蛋白-配体复合物分辨率低于0.3 nm,将选中的蛋白-配体晶体机构下载保存。利用PyMOL软件对蛋白质进行去水、去...
2.6分子对接预测白屈菜碱、延胡索乙素和阿霉素与细胞焦亡相关蛋白的结合活性 首先从蛋白质结构数据库(protein data bank,PDB)数据库(https: //www.rcsb.org)中检索关键靶点蛋白信息,根据蛋白结构的分辨率、完整性、结合口袋的形状、大小...
interactions or, as is the case for NLRP3, via the bipartite adapter, apoptosis-associated speck-like protein containing a CARD (ASC). Subsequently, Caspase-1 undergoes proximity-induced autoproteolysis and cleaves IL-1β, as well as the related IL-1 family member, IL-18, to release their ...
caspase-11 (C254A)-p22/p10 结构(PDB ID 代码 6KMU)用作小鼠 CASP11 (p22/p10) 模型。基于全长鼠 GSDMD(PDB ID 代码 6N9N)的结构,程序 Modeler 生成了带有切割接头的全长 mGSDMD 中鼠 GSDMD-N 片段的失活构象(mGSDMD-Ni)。此外,基于小鼠 GSDMA3(PDB ID 代码 6CB8)和人类 GSDMD(PDB ID 代码 6...
The PDB format of NLRP3 (ID: 6npy) [14] was downloaded from RCSB (https://www.rcsb.org/), waters and het groups were deleted, and hydrogens were added, and then the docking procedure was submitted [15]. 2.2. Animals Male Sprague-Dawley (SD) rats were purchased from Pizhou Oriental...
Three-dimensional crystal structure was retrieved from PDB database. This structure was optimized prior to docking using the Protein Preparation Wizard in Schrodinger Maestro11.0. Inconsistencies in the structure such as missing hydrogen, incorrect bond orders, orientation of the different functional groups...
1etter to the editor caspase c1eavage sites in the human proteome caspdb a database of predicted substratesof our paper.piotrcieplak
利用PyMOL软件对蛋白质进行去水、去磷酸根等操作,保存为PDB文件。采用Molecular Operating Environment 2019软件对化合物进行能量最小化,对靶点蛋白进行预处理并寻找活性口袋,进行半柔性分子对接,根据结合能大小评估二者的结合活性,并将结果通过PyMOL、Discovery studio软件进行可视化处理。
首先从蛋白质结构数据库(protein data bank,PDB)数据库(https: //www.rcsb.org)中检索关键靶点蛋白信息,根据蛋白结构的分辨率、完整性、结合口袋的形状、大小和化学性质以及蛋白结构的共晶配体等相关信息,确定蛋白结构。利用PyMOL软件去除靶点蛋白的水分子和配体。然后利用PubChem数据库检索并下载该化学成分的二维结构图...
Modeling of LZ-C9 A molecular model of LZ-C9 was constructed using the GCN4 leucine-zipper coordinates (PDB ID 2ZTA) and caspase-9 coordinates (P...Stennicke HR , Salvesen GS ( 2000 ) Caspase assays . Methods Enzymol 322 : 91 – 100Caspase assays[J] . Henning R. Stennicke,Guy S....