Computational protocol: Bioinformatic Identification of Peptidomimetic-Based Inhibitors against Plasmodium falciparum Antigen AMA1

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Protocol publication

[…] The modeled peptides were docked on the hydrophobic groove containing region of PfAMA1 (PDB ID: 1Z40) with AutoDock Vina program (Molecular Graphics Laboratory) [] on Windows platform. The best models of the peptides with zero root mean square deviation (RMSD) values were used for docking studies. To prepare the receptor for docking, PDB file of the receptor was opened in AutoDock Vina, water molecules were removed, polar hydrogens were added, and the receptor was saved as PDBQT file. To prepare the ligand, PDB file of the ligand was opened in AutoDock Vina and saved as PDBQT file. Grid parameters used for docking were 54 Å × 30 Å × 56 Å. [...] Virtual screening of peptidomimetics against the crucial residues of PfAMA1 implicated in binding with PfRON2 peptide (residues Pro-2033, Phe-2038 to Arg-2041, and Pro-2044) was carried out with pepMMsMIMIC server []. This server is based on multiconformer, three-dimensional (3D) similarity search using as input the 3D structure of a peptide bound to a protein and suggests which chemical structures are able to mimic this natural interaction. Scoring method used was fingerprint-based filtering of shape similarity taking the side chain interactions into consideration. […]

Pipeline specifications

Software tools AutoDock Vina, pepMMsMIMIC
Applications Drug design, Protein interaction analysis
Organisms Plasmodium falciparum