Selected article for: "local protein protein docking starting complex and low energy"
Author: Qiang Huang; Andreas Herrmann
Title: Fast assessment of human receptor-binding capability of 2019 novel coronavirus (2019-nCoV)
  • Document date: 2020_2_3
    • ID: eecyduzq_35
    Snippet: And the Rosetta all-atom energy function 2015 (REF15) (Alford et al., 2017) Local protein-protein docking. The docking program of Rosetta (Das and Baker, 2008) was used to carry out the local protein-protein docking with the starting conformation of a given S-RBD-ACE2 complex. The Rosetta energy function 2015 (REF15) was employed in the docking to evaluate the interaction energy of two docking components (i.e., S-RBD and ACE2). For each S-RBD-ACE.....
    Document: And the Rosetta all-atom energy function 2015 (REF15) (Alford et al., 2017) Local protein-protein docking. The docking program of Rosetta (Das and Baker, 2008) was used to carry out the local protein-protein docking with the starting conformation of a given S-RBD-ACE2 complex. The Rosetta energy function 2015 (REF15) was employed in the docking to evaluate the interaction energy of two docking components (i.e., S-RBD and ACE2). For each S-RBD-ACE2 pair, at least 3,000 independent docking simulations were performed to generate a large number of thermodynamically probable, low-energy binding conformations for calculating the binding freeenergy. The top-scoring, lowest-energy conformations were identified as the native-like conformations of the S-RBD binding to ACE2. The local protein-protein docking protocols are:

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