Computational protocol: The complete N terminal extension of heparin cofactor II is required for maximal effectiveness as a thrombin exosite 1 ligand

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Protocol publication

[…] Molecular modeling of the first 75 amino residues of human HCII was performed using 3D-Jigsaw Comparative Modeling software [] in the automatic mode. This software makes use of a threading algorithm dependent on secondary structure prediction by PSIPRED []. The predicted HCII1-75 molecular model fell within the 95th percentile for expected structural accuracy (E value of 5.0 x 10-5). Structural superimposition was performed with COOT []. Images were prepared with PyMol (The PyMOL Molecular Graphics System, Version 1.2, Schrödinger, LLC). […]

Pipeline specifications

Software tools PSIPRED, Coot, PyMOL
Application Protein structure analysis
Organisms Escherichia coli