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Fig. 5 | Journal of Cheminformatics

Fig. 5

From: Chemoinformatics and structural bioinformatics in OCaml

Fig. 5

Overview of EleKit applied to PDB codes 2B4J (\(1_{A}\)) and 3LPU (\(1_{B}\)). The “ligand-protein” is shown as a green surface in \(1_{A}\) and \(2_{A}\). The “ligand-small-molecule” is shown as a smaller green surface in \(1_{B}\) and \(2_{B}\). The receptor protein is shown as a gray cartoon in \(1_{A}\) and \(1_{B}\). Electrostatic potential fields are calculated and stored in distinct grids (\(2_{A}\) and \(2_{B}\)). A boolean mask in 3D is created to select the solvent region nearby the interface (\(3_{A}\) and \(3_{B}\)). Finally, the similarity between electrostatic potentials in the masked region (\(4_{A}\) and \(4_{B}\)) is calculated using the Spearman rank correlation coefficient (figure adapted from Voet [26])

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