Result Recovery for FE-NES

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Product-based/Molecular Dynamics

  • Role-based/Computational Chemist

  • Role-based/Medicinal Chemist

  • Task-based/Molecular Dynamics

  • Task-based/Affinity Prediction

  • Solution-based/Hit to Lead/Affinity Prediction/Free-Energy Calculations

  • Solution-based/Small Molecule Lead-opt/Affinity

Description

  • Purpose:

    • This floe allows for the recovery of free-energy nonequilibrium switching (FE-NES) results in case the FE-NES Floe hangs.

  • Method Recommendations/Requirements:

    • Two primary inputs are required; one additional primary input is optional. All other fields are supplementary:

      • The recovery file from the FE-NES Floe that hung.

      • Orion datasets containing equilibrium run data for each ligand participating in the FE-NES run.

      • [Optional] Select experimental binding affinities from the Orion dataset containing equilibrium run data, or supply a text file containing ligand names, affinity values, optional uncertainties, and optional units.

  • Expertise Level:

    • Regular

  • Compute Resource:

    • Minimal

  • Keywords:

    • Utility, FECalc

  • Related Floes:

    • FE-NES for Binding Affinity Prediction

This floe is used to recover the FE-NES results in case the FE-NES Floe hangs. Using as input the recovery file from FE-NES, it will complete the analysis of the FE-NES results to produce the same output datasets as FE-NES. The analysis will be based only on the data in the recovery file.

Promoted Parameters

Title in user interface (promoted name)

Inputs

End-State MD Simulations (equilibrium): With default naming, this input will be named md_output/md_output_with_analysis (current) or MD_Bnd_Anlys/MD_Bnd and MD_Unb_Anlys/MD_Unb (legacy bound/unbound MD) in an upstream floe.

  • Required

  • Type: data_source

NES Recovery File (recovery): With default naming, this input will be named fe_nes_recovery_binary in an upstream floe.

  • Required

  • Type: file_in

Experimental Affinities (From Equilibrium Dataset)

Column in the dataset with experimental affinity values (affinity_column): Populated after selecting the dataset.

  • Type: field_parameter::any

  • Default: —

Units for affinity values (units):

Use ‘log’ for pIC50, pKi, etc.

  • Type: string

  • Default: Not selected

  • Choices: [‘Not selected’, ‘kcal/mol’, ‘kJ/mol’, ‘pM’, ‘nM’, ‘uM’, ‘mM’, ‘M’, ‘log’]

Column in the dataset with experimental affinity uncertainties (affinity_error_column): Populated after selecting the dataset.

  • Type: field_parameter::float

  • Default: —

Experimental Affinities (From Text File)

Text File Containing Experimental Affinities (exp):

Syntax for ASCII file: [Ligand] [Affinity] [Error {optional}] [units {optional}]. Allowed units: kcal/mol, kJ/mol, log, M, mM, uM, nM, pM. Use ‘log’ for pIC50, pKi, etc. Use ‘M’, ‘mM’, ‘uM’, ‘nM’ or ‘pM’ for IC50, Ki, etc.

  • Type: file_in

Delimiter (field_separator): Select whether the file is delimited by whitespace (including tabs) or commas. Delimiters cannot be mixed.

  • Type: string

  • Default: whitespace(s)

  • Choices: [‘whitespace(s)’, ‘,’]

Units for affinity values (units_expt_file):

Use ‘log’ for pIC50, pKi, etc. Units present in the experimental file override this selection.

  • Type: string

  • Default: Not selected

  • Choices: [‘Not selected’, ‘kcal/mol’, ‘kJ/mol’, ‘pM’, ‘nM’, ‘uM’, ‘mM’, ‘M’, ‘log’]

Outputs

Affinity Output Dataset (affinity_out): Primary output containing per-molecule affinity predictions computed from the relative affinity predictions.

  • Required

  • Type: dataset_out

  • Default: affinity_predictions

Relative Affinity Output Dataset (nes_out): Output containing pairwise relative affinity predictions computed.

  • Required

  • Type: dataset_out

  • Default: relative_affinity_predictions

FE-NES Result Archive (nes_results_archive): Tar.gz archive containing FE-NES calculation results.

  • Required

  • Type: dataset_out

  • Default: fe_nes_results_archive

Affinity Predictions Report (affinity_floe_report): Title for the affinity predictions floe report.

  • Type: string

  • Default: Affinity Predictions Report

Relative Affinity Predictions Report (relative_affinity_floe_report): Title for the relative affinity predictions floe report.

  • Type: string

  • Default: Relative Affinity Predictions Report

Edge Map Diagram With Predictions (edge_map_with_pred_floe_report): Title for the edge map diagram with predictions floe report.

  • Type: string

  • Default: Edge Map Diagram with Predictions

Failed Output Dataset (fail_out): Stores information about failed calculations.

  • Required

  • Type: dataset_out

  • Default: Failed Output for Result Recovery for FE-NES