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Insights into interactomics-driven drug repurposing to combat COVID-19
Published in Sanjeeva Srivastava, Multi-Pronged Omics Technologies to Understand COVID-19, 2022
Amrita Mukherjee, Ayushi Verma, Ananya Burli, Krishi Mantri, Surbhi Bihani
PyMOL is a powerful open-source software for visualization scripted in Python, C, and C++ and created by Warren Lyford DeLano. The application, maintained and distributed by Schrödinger, is available for installation on various operating systems like macOS, Windows, Unix, and Linux.
Co(II)-coordination polymer: treatment and nursing values on trachoma by inhibiting the Chlamydia trachomatis survival
Published in Inorganic and Nano-Metal Chemistry, 2022
Yan Yang, Lei Shao, Dong-Li Zhao
For the preparation of the molecular docking simulation, the donator complex and the receptor protein were prepared separately. The structure of the complex was obtained directly from experimental results, and the structure of the receptor was C-terminal domain of the RNA polymerase alpha subunit and downloaded from the protein data bank, the raw structure of the downloaded protein is 3GFK,[29] which is an interacting complex containing the Bacillus subtilis Spx protein and the C-terminal domain of the RNA polymerase alpha subunit, then the irrelevant Bacillus subtilis Spx protein was removed from 3GFK and left with the desired C-terminal domain of the RNA polymerase alpha subunit. Regarding the setup of the simulation, the grid box is 80 angstrom in length and the coordinates of gird center are 56.065, 0.471 and 0.432 in three dimensions, respectively. The preparation was performed by AutoDockTools and the molecular docking simulation was performed by AutoDock 4, the visualization of the docking poses was rendered by open source version of PyMOL.
Self-assembled peptide-conjugated rosemary extract derivatives as drug delivery vehicles for targeting tumor cells
Published in Soft Materials, 2022
Lucy R. Hart, Saige M. Mitchell, Paige A. McCallum, Rachel E. Daso, Ipsita A. Banerjee
Predictions of ligand interactions with known structural models of receptors were performed utilizing the AutoDock Vina plugin on Pymol 2.4.0. AutoDock Vina is a molecular docking software that uses a multi-threading technique to evaluate the binding mode of a receptor and ligand.[33] The program was used in conjunction with AutoDockTools suite which is a graphical user interface that creates the proper formatting of molecules to input into AutoDock Vina.[34] The receptors were prepared utilizing AutoDockTools- 1.5.7 by uploading the PDB files obtained from the RCSB Protein Data Bank, followed by deleting water molecules, adding polar hydrogens and Kollman charges, and saving the molecule as a .pdbqt file. Then, the ligands (RMA-peptide and CSA-peptide conjugates) were prepared by initially drawing the structures on ChemDraw 19.1 and minimizing their energy utilizing ChemDraw 3D. The files were then uploaded onto AutoDockTools- 1.5.7 and selected for molecular docking analyses. The parameters for each grid (40 x 40 × 40) were created automatically in the software to determine the most likely docking site for the ligands. For each ligand, eight iterations were run. The results of the studies revealed binding affinities for each ligand with the given receptor. The output files for docking studies were visualized on PyMOL 2.4.0. to determine hydrogen bond lengths and binding residues. Studies were performed to examine binding interactions between estrogen receptors, SRC kinase receptors, with CSA-peptide, and RMA-peptide conjugates as the ligands.
In-silico investigation of the efficiency of microbial dioxygenases in degradation of sulfonylurea group herbicides
Published in Bioremediation Journal, 2022
Sutapa Bauri, Madhab Kumar Sen, Renuka Das, Sunil Kanti Mondal
For structural analysis, CASTp bioinformatics tool (Computed Atlas of Surface Topography of proteins; http://sts.bioe.uic.edu/castp) was used to determine surface topography of the proteins (Tian et al. 2018). The 3 D structures of dioxygenases from Pseudomonas putida (1MPY), Brevibacterium fuscum (1F1X), Arthrobacter globiformis (1F1R) were collected from Protein Data Bank (PDB; http://www.rcsb.org/pdb) (Berman et al. 2000). Furthermore, structure alignment was also performed to see structural similarity among the structures of the selected proteins using PyMOL (version 2.1.0) (https://pymol.org/2/).