pKa Exploration Floe
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Role-based/Computational Chemist
Role-based/Medicinal Chemist
Solution-based/Hit to Lead/Properties/pKa
Task-based/Library Prep & Design
Description
This floe predicts values of the pKa (the log of the acid dissociation constant, Ka) and generates detailed reports on all micro- and macro-pKas predicted, titration curves, protonation micro-equilibria, and a summary of significant states at each macrostate level. It also includes macro- and microspeciation curves and a LogD plot for pH 0.0 to 14.0. This floe is intended to run on a set of up to a few hundred molecules, since it generates quite large reports, including images and plots.
Promoted Parameters
Title in user interface (promoted name)
Inputs
Small Molecule Dataset to Predict pKa On (new_mols): Small molecule dataset to predict pKa on.
Required
Type: data_source
Outputs
Macro-pKa Prediction (macro_pka_pred): Dataset with macro-pKa prediction.
Required
Type: dataset_out
Default: Macro-pKa
Significant Microstates (significant_micro_states): Dataset of significant microstates.
Required
Type: dataset_out
Default: Significant micro-states
Significant ionization state molecule field (Ionization_state_field): The field to store the significant state of the molecule. By default it replaces the PrimaryMolField.
Type: field_parameter::mol
Failed Descriptors Calculation (newmols_desc_failed): Dataset of molecules with failed descriptors calculation.
Required
Type: dataset_out
Default: Descriptors failed
Options
Get multiple significant states (get_multiple_states): Choose whether to generate multiple significant states at chosen environment pH and fraction cutoffs
Required
Type: boolean
Default: False
Choices: [True, False]
Calculate LogD (calc_logD): Choose whether to calculate LogD value
Required
Type: boolean
Default: True
Choices: [True, False]
Environment pH (env_pH): pH of environment in which micro states of the molecule are to be estimated
Required
Type: decimal
Default: 7.4
Choices: [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0]
Advanced options
Cutoff for ionizable groups count (ion_groups_count_cutoff): The maximum number of ionizable groups to be processed in detailed micro/macro-pKa prediction and protonation micro-equilibria. These groups are chosen by estimated intrinsic pKa to be around chosen environment pH (default 7.4).
Required
Type: integer
Default: 4
Choices: [2, 3, 4, 5]
Percentage cutoff for macro-state (macro_state_fraction_cutoff): Only macro states higher than this percentage cutoff at chosen environment pH will be saved to significant states output dataset.
Required
Type: integer
Default: 20
Choices: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99]
Percentage cutoff for micro-states within the macro state (tautomer_fraction_cutoff): Only micro states having fraction (tautomer fraction) higher than this percentage cutoff within a selected macro state, will be saved to significant states output dataset.
Required
Type: integer
Default: 35
Choices: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99]
Supporting experimental pKa data file (supporting_data_filename): Name of the supporting data descriptors file you have already created using the floe ‘Prepare supporting experimental pKa data file’
Type: file_in