Knime/RDKIT/MGLTools/PDB2PQR/Autodock Vina
Knime/RDKIT/MGLTools/PDB2PQR/Autodock Vina
Assumed pH 7.0
flexible ligand
Gasteiger method used to compute charge on ligand
Knime was used to read the Smiles, we generated the coordinates throught the RDKIT node for each ligand. Each ligand was protonated with Autodock Tools at pH 7.0 using Gasteiger method. We used PDB2PQR server to compute charge on receptor using AMBER99 force field. The screening and scoring steps were performed by Autodock Vina on twelve different structures extracted from a clustering analysis of BACE1 dynamic. The mean of these scores was computed to rank ligand by their energy of interaction with BACE1.
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