Author: Fabiana Renzi; Dario Ghersi
Title: ACE2 fragment as a decoy for novel SARS-Cov-2 virus Document date: 2020_4_10
ID: 77ku0164_28
Snippet: Docking experiments and interaction energy calculations were carried out using RosettaDock (12, 13) . To obtain the per-residue energy breakdown of the ACE2/S-protein complex we relaxed the structure to relieve clashes using the flag_input_relax protocol provided with the Rosetta suite. We then optimized the complex by performing 1,000 redocking experiments with the local docking protocol provided in the suite, and selected the pose with the most.....
Document: Docking experiments and interaction energy calculations were carried out using RosettaDock (12, 13) . To obtain the per-residue energy breakdown of the ACE2/S-protein complex we relaxed the structure to relieve clashes using the flag_input_relax protocol provided with the Rosetta suite. We then optimized the complex by performing 1,000 redocking experiments with the local docking protocol provided in the suite, and selected the pose with the most favorable interaction energy. The per-residue energy breakdown was obtained with the residue_energy_breakdown provided in the suite. For the docking experiment with angiontensinII, we used the ligand found in the crystal structure of the complex with the ACE receptor (pdb:4APH, chain P) superposed onto the crystal structure of ACE2. After relaxing the complex, we carried out 1000 docking experiments and retained the pose with the most favorable interaction energy.
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