Fast assessment of human receptor-binding capability of 2019 novel coronavirus (2019-nCoV)

Qiang Huang; Andreas Herrmann

(2011), the co-crystal structure of SARS-CoV S-RBD in complex with ACE2 (PDB 2AJF) was used as the starting complex for the local protein-protein docking. Then, more than 3,000 independent docking runs were conducted to sample the low-energy binding conformations by optimizing rigidbody orientation and side-chain conformations, according to the docking protocols in Methods. The binding free-energy scores of the obtained complex models are shown in the scatter plot in Fig. 1A , against their RMSD (root mean square deviation) values of interface residues with respect to those in the starting co-crystal structure. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.01.930537 doi: bioRxiv preprint 5 As seen, a deep energetic funnel exhibits in the plot, and therefore clearly indicates that the docking simulations are very successful, because the presence of such a funnel is the most robust measure of successful docking simulations (Chaudhury et al., 2011) . Due to their locations at the funnel bottom, the top-scoring models have better binding free-energy scores than other low-energy models, and therefore are considered to be the most probable, native-like binding conformations in thermodynamics.