导入复合物 复制表格 下载口袋,下载图片 2D相互作用: Protein-Ligand Interaction Profiler https://proteins.plus/ posview查看相互作用 点击ligiand 其他功能:预测活性口袋的位点 DoGSiteScorer Binding site detection 后期pymol的处理: 鼠标中键可以切换为selecting residues 重命名残基rename selection> label<residues...
Protein structures were examined using Pymol (Schrödinger, Inc.). The solvent accessible area was calculated using the program Naccess (S. Hubbard, University of Manchester, UK). The figures showing structures colored by association constant (Figs. 2, 4) were produced as putty plots in Py...
59and the images were generated by PyMOL60. The protein chains in the complexes are colored in light blue while the peptide chains are colored in light purple and pink. For each peptide, the true binding residues are colored in pink while the predicted binding residues generated by CAMP are...
bioinformaticspymol-pluginpymolprotein-sequencessequence-alignmentshomology-modelingprotein-structuresstructural-alignmentssimilarity-searches UpdatedMay 29, 2024 Python sbl-sdsc/mmtf-pyspark Star67 Code Issues Pull requests Methods for the parallel and distributed analysis and mining of the Protein Data Bank...
下载完之后,可以通过VMD、Chimera、PyMOL等可视化软件查看其结构。接下来需要去除文件中的结晶水、PO4和BME。这一步并不是一个必须步骤,只有不需要结晶水的时候才需要去除,而如果特意研究结晶水就不能去除。在本例中我们并不需要结晶水或者其他结晶的共溶剂。就下来重点关注JZ4配体,即2-丙基苯酚(2-propylphenol)。
load_pdb('/tmp/1EVE.pdb') # Load the PDB file into PLIP class print(my_mol) # Shows name of structure and ligand binding sites my_bsid = 'E20:A:2001' # Unique binding site identifier (HetID:Chain:Position) my_mol.analyze() my_interactions = my_mol.interaction_sets[my_bsid] # ...
Potential surfaces were generated by the APBS program (Baker et al., 2001) and were displayed by PyMOL (http://www.pymol.org). Using 100 representative configurations of the transition-state ensemble, the electrostatic interaction free energy was calculated by solving the linearized Poisson-...
All Euclidean distances in angstroms (Å) between peptide atoms and chemical compound atoms included in the PDB files were calculated with custom-made PyMOL-Python scripts and PERL scripts. The minimum distance found between the MS-detected peptide and the investigated metabolite was reported as ...
Alongside with a set of customizable parameters, KVFinder brings an innovative, easy to use, graphical interface implemented as a PyMOL Plugin. The interface has a basic mode tab, the one click analysis, which displays a limited group of options to set up small and big probe sizes, grid ...
in the protein interior. An embedded triplet clique (from 3F67.pdb) constituted of 119-Phe (Olive), 142-Trp (Lime) and 143-Tyr (Yellow) displayed as sticks in a background of broken stretches of the backbone being displayed as cartoon (Cyan). The image was constructed using PyMol [44...