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AutoDock Gateway for Molecular Docking Simulations in Cloud Systems
Published in Olivier Terzo, Lorenzo Mossucca, Cloud Computing with e-Science Applications, 2017
Zoltán Farkas, Péter Kacsuk, Tamás Kiss, Péter Borsody, Ákos Hajnal, Ákos Balaskó, Krisztián Karóczkai
AutoDock Vina provides several enhancements over AutoDock4, increasing average simulation accuracy while also being up to two orders of magnitude faster. Autodock Vina is particularly useful for virtual screening, whereby a large set of ligands can be compared for docking suitability with a single receptor. In this instance, parallelism is achieved by first breaking the set of all ligands into equal-size disjoint subsets. Each compute job then uses a different subset as an input. The ligands in each subset are simulated/docked sequentially on the compute node using the single receptor; a postprocessing stage can be used to compare the results from all compute jobs.
A new 3D zinc (II)-coordination polymer: treatment activity on lymphoma combined with doxorubicin via regulating apoptotic genes expression
Published in Inorganic and Nano-Metal Chemistry, 2021
Xin-Sheng Han, Ting Li, Xing-An Zhang, Jun Lu
All molecular docking simulations were performed by using the AutoDock 4 software package. To investigate the biological activity of the Zn(II) complex, the Bcl-2 protein has been chosen as the probe protein, explicitly, the solution structure of the anti-apoptotic protein Bcl-2 has been downloaded from protein data bank, the PDB ID is 1YSW. As mentioned in the experimental section, the Zn(II) complex exhibits an asymmetry structure, which contains two different types of moieties, the former one mainly contains the carbonyl functional group while the latter one mainly contains the structure containing nitrogen atom, it has been suggesting that the two types of moieties may present completely different activities to the probe protein, so in the current study, the two types of moieties associated with the Zn(II) metal core have been used as the ligands for the investigation of the biological activity. The center of the docking pocket locates at the 7.868, −4.221, and −3.846 Å. All other parameters are using as the default if not mentioned specifically.
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.
A new mixed-ligand Co(II) coordination polymer: treatment activity on ulcerative colitis by inhibiting the JAK2/STAT3 signaling pathway in the colonic epithelial cells
Published in Inorganic and Nano-Metal Chemistry, 2021
Yan Tan, Hong-Yu Yun, Jing Tang, Du-Xiong Cai, Xiao-Ning Sun
The molecular docking simulation has been performed by using AutoDock 4. The preparation of the docking simulation is completed by the AutoDockTools. The probe protein is 5UT1 (PDB ID) which has been downloaded from the protein data bank, postprocessing treatment including removing the water and ligands has been performed before using it as the probe protein. The complex has been treated as the semiflexible ligand, meaning the rotation of single bond is allowed. The grid box length is 80 Å which is large enough for performing the configuration scoring, the center of the grid box is—2.474, 25. 053, and 14.410 Å. Other parameters are using as default.