Selected article for: "software package and stereochemical structural quality"
Author: Thomas Desautels; Adam Zemla; Edmond Lau; Magdalena Franco; Daniel Faissol
Title: Rapid in silico design of antibodies targeting SARS-CoV-2 using machine learning and supercomputing
  • Document date: 2020_4_10
    • ID: kg2j0dqy_32
    Snippet: In the constructed final models, the conformation of sidechain atoms was predicted using SCWRL [29] when residue-residue correspondences did not match. Residues that were identical between the template and the SARS-CoV-2 spike protein were copied from the templates onto the models. The structural and stereochemical quality of the models was checked using a contact-dot algorithm in the MolProbity software package [30] , and the final constructed m.....
    Document: In the constructed final models, the conformation of sidechain atoms was predicted using SCWRL [29] when residue-residue correspondences did not match. Residues that were identical between the template and the SARS-CoV-2 spike protein were copied from the templates onto the models. The structural and stereochemical quality of the models was checked using a contact-dot algorithm in the MolProbity software package [30] , and the final constructed models were finished with relaxation using UCSF Chimera [31] . Figures 4 and 5 show two of our constructed structural models of the SARS-CoV-2 spike protein in complex with a FAB (S230 and M396 in Figs. 3 and 4, respectively) of a SARS-CoV-1 neutralizing antibody. A set of all provided models was constructed to help assessment of possible different conformations in the spike-antibody complexes.

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