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Binding Pose Metadynamics

Workflow

Metadynamics Analysis of Binding Poses

Various binding configurations of a single ligand in a single binding site are ranked.

Molecular Dynamics
- MetadynamicsBinding_CompScoreComposite Score linearly combining the r_psp_MetadynamicsBinding_PoseScore and -MetadynamicsBinding_Persistence scores. Lower values equate to more stablecomplexes. The equation is PoseScore - 5 * Persistence- MetadynamicsBinding_PoseScoreExpectation of the RMSD of the pose over the course of the metadynamics. Lower valuesequate to more stable complexes.- MetadynamicsBinding_PersistenceAverage persistence of contacts over the course of the metadynamics trajectories. Highervalues equate to more stable complexes- MetadynamicsBinding_Persistence_HBondAverage persistence of HBonds- MetadynamicsBinding_Persistence_PiAverage persistence of Pi-Pi stacking and T-Shaped interactions- MetadynamicsBinding_In_RMSD -- Optional RMSD after the relaxation step. This can helpidentify cases where the relaxation before the metadynamics is materially changing thepose Metadynamics Analysis of Binding PosesVarious binding configurations of a single ligand in a single binding site are ranked.Binding pose metadynamicsHeight, Trial and hostsProtein-ligandcomplexesbinding_pose_metadynamics.py Highlight the ligands to ignore when they are several ASL res.ptypePrimemetadynamics Composite score,Pose score and persistence scores Text output logBinding Pose Metadynamics jobsChemistryExternal Tool Configuration Molecule Reader(to MAE) Get Help Table Viewer Table Viewer Ligand ASL Extract Properties Table Viewer Column Resorter Transpose Table Viewer Table Viewer Job Control - MetadynamicsBinding_CompScoreComposite Score linearly combining the r_psp_MetadynamicsBinding_PoseScore and -MetadynamicsBinding_Persistence scores. Lower values equate to more stablecomplexes. The equation is PoseScore - 5 * Persistence- MetadynamicsBinding_PoseScoreExpectation of the RMSD of the pose over the course of the metadynamics. Lower valuesequate to more stable complexes.- MetadynamicsBinding_PersistenceAverage persistence of contacts over the course of the metadynamics trajectories. Highervalues equate to more stable complexes- MetadynamicsBinding_Persistence_HBondAverage persistence of HBonds- MetadynamicsBinding_Persistence_PiAverage persistence of Pi-Pi stacking and T-Shaped interactions- MetadynamicsBinding_In_RMSD -- Optional RMSD after the relaxation step. This can helpidentify cases where the relaxation before the metadynamics is materially changing thepose Metadynamics Analysis of Binding PosesVarious binding configurations of a single ligand in a single binding site are ranked.Binding pose metadynamicsHeight, Trial and hostsProtein-ligandcomplexesbinding_pose_metadynamics.py Highlight the ligands to ignore when they are several ASL res.ptypePrimemetadynamics Composite score,Pose score and persistence scores Text output logBinding Pose Metadynamics jobsChemistryExternal Tool Configuration Molecule Reader(to MAE) Get Help Table Viewer Table Viewer Ligand ASL Extract Properties Table Viewer Column Resorter Transpose Table Viewer Table Viewer Job Control

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Nodes

Binding Pose Metadynamics consists of the following 33 nodes(s):

Plugins

Binding Pose Metadynamics contains nodes provided by the following 4 plugin(s):