Computational protocol: ICP35 Is a TREX-Like Protein Identified in White Spot Syndrome Virus

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Protocol publication

[…] To characterize the function of ICP35, automated homology modeling was performed by using the SWISS-MODEL server []. Crystal structure of three prime repair exonuclease I (TREX1) (PDB ID: 3b6o with 2.10 Å resolution) was used as a template, All pictures of the ICP35 model were created in PyMOL. To validate the model, the internal molecular mechanics (MM) energy and implicit solvent solvation energy have been calculated using AMBER99 force field parameters and generalized-Born surface energy approximation (GB/SA) method for the structures of ICP35 monomer and ICP35 dimer after performing an energy minimization in explicit solvent. The pairwise GB/SA energy decomposition was performed by using a python script freely available in the AmberTools15 package to elucidate the energetic contribution of the conserved salt bridge and hydrogen bonding residues. […]

Pipeline specifications

Software tools SWISS-MODEL, PyMOL, AMBER
Application Protein structure analysis
Organisms Escherichia coli
Diseases Dental Caries