Convert MD Analysis results to Cluster-Centric Dataset [Utility]ΒΆ

Category Paths

  • 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/STMD

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


  • Purpose:

    • This Floe postprocesses a dataset from protein-ligand MD analysis to convert it into a cluster-centric dataset suitable to be used as input to other Floes.

  • Method Recommendations/Requirements:

    • Input is an output dataset from a protein-ligand MD analysis Floe: * Short Trajectory MD with Analysis * Analyze Protein-Ligand MD

  • Limitations

    • The resulting cluster-centric dataset is not intrinsically ordered by ligand, but this can be done in the spreadsheet of the Analyze page.

  • Expertise Level:

    • Regular

  • Compute Resource:

    • Minimal

  • Keywords:

    • Utility

  • Related Floes:

    • Analyze Protein-Ligand MD [MDAnalysis]

    • Short Trajectory MD with Analysis [MDPrep] [MD]

The results datasets output from the protein-ligand MD analysis Floes is ligand-centric, containing cluster information inside. To be able to select specific clusters to carry forward as input to another Floe, this ligand centric dataset must be converted by this Floe into a cluster-centric dataset.

Promoted Parameters

Title in user interface (promoted name)

  • Failed Dataset (fail) type: dataset_out: Output dataset of failed calculations
    Default: failed_dataset
  • MD Analysis Input Dataset (in) type: data_source: Input dataset from MD Analysis
  • Cluster-Centric Dataset (out) type: dataset_out: Output cluster-centric dataset
    Default: cluster_centric_dataset