Computational protocol: Human Transbodies to HCV NS3/4A Protease Inhibit Viral Replication and Restore Host Innate Immunity

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Protocol publication

[…] Three-dimensional structure of NS3/4A (PDB ID-1A1R, RCSB database) was retrieved. Tertiary structures of HuscFvs were modeled by subjecting their amino acid sequences to the I-TASSER server (). The I-TASSER-predicted models were subsequently refined and improved to their nearest native state (, ). Molecular docking between the NS3/4A 3D and the HuscFv models was performed by ClusPro2.0 server (). Pymol software (The PyMOL Molecular Graphics System, version 1.3r1 edu, Schrodinger, LLC) was used to build and visualize the protein complexes that formed the largest cluster size and the minimal local energy. […]

Pipeline specifications

Software tools I-TASSER, Cluspro, PyMOL
Application Protein interaction analysis
Organisms Homo sapiens, Escherichia coli
Diseases Hepatitis C
Chemicals Zinc