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Fig. 1 | Journal of Cheminformatics

Fig. 1

From: Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules

Fig. 1

A schematic representation of the dimorphite-DL approach. Each ionizable moiety is associated with a pKa range (rangePKA) defined by three parameters: µ, σ, and n. The user specifies a pH range (rangepH) and pKa precision factor (n; default: 1.0). The mean (µ) and standard deviation (σ) associated with each moiety are derived from the database of small molecules with experimentally characterized pKa values. If rangePKA is entirely less than rangepH, dimorphite-DL outputs a deprotonated molecule. If rangePKA is entirely greater than rangepH, dimorphite-DL outputs a protonated molecule. If rangePKA and rangepH overlap, dimorphite-DL outputs both deprotonated and protonated molecules

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