Computational protocol: The Kunitz-Type Protein ShPI-1 Inhibits Serine Proteases and Voltage-Gated Potassium Channels

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Protocol publication

[…] Sequences and three-dimensional (3D) structures of ShPI-1 and other toxins here analyzed were retrieved from the UniProt/Swiss-Prot and the Protein Data Bank (PDB) databases respectively. ClustalOmega [] was used for multiple sequence alignment. Structural comparisons were performed using PDBeFold []. The interatomic contacts and accessible surface area (ASA) relative to the residue in a vacuum were calculated using WHAT IF []. […]

Pipeline specifications

Software tools Clustal Omega, PDBeFold
Databases UniProt
Application Protein structure analysis
Organisms Bos taurus
Chemicals Amino Acids, Cysteine, Potassium