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Database preparation Property calculation | ||||
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Database preparation Property calculation | ||||
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Filter has a rule-based system to set the ionization state of input molecules. This feature is controlled with the pKaNorm command-line parameter. If pKaNorm is true, the program attempts to set each molecule to its most energetically favorable ionization state for pH=7.4. The rule-based nature of this calculation allows it to be quite fast. Further, despite being rule-based, this approach takes into account many secondary charge interactions. While more advanced levels of theory can be found for predicting ionization states, we feel this method is very well suited to virtual-screening database preparation. However, for hit-to lead or lead optimization we would recommend a higher level of theory for both primary pKa estimation (Hammet-Taft or experiment) and formal-charge to formal-charge interactions (Poisson-Boltzmann). Finally, given the level of detail at which it is practicle to carry out calculations for a high-throughput, consistency is in ones approach is a significant virtue.
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Database preparation Property calculation | ||||
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