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PyLipID documentation
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  • Installation
  • Documentation
    • pylipid.api
      • pylipid.api.LipidInteraction.collect_residue_contacts
      • pylipid.api.LipidInteraction.compute_residue_duration
      • pylipid.api.LipidInteraction.compute_residue_occupancy
      • pylipid.api.LipidInteraction.compute_residue_lipidcount
      • pylipid.api.LipidInteraction.compute_residue_koff
      • pylipid.api.LipidInteraction.compute_binding_nodes
      • pylipid.api.LipidInteraction.compute_site_duration
      • pylipid.api.LipidInteraction.compute_site_occupancy
      • pylipid.api.LipidInteraction.compute_site_lipidcount
      • pylipid.api.LipidInteraction.compute_site_koff
      • pylipid.api.LipidInteraction.analyze_bound_poses
      • pylipid.api.LipidInteraction.compute_surface_area
      • pylipid.api.LipidInteraction.write_site_info
      • pylipid.api.LipidInteraction.show_stats_per_traj
      • pylipid.api.LipidInteraction.save_data
      • pylipid.api.LipidInteraction.save_coordinate
      • pylipid.api.LipidInteraction.save_pymol_script
      • pylipid.api.LipidInteraction.plot
      • pylipid.api.LipidInteraction.plot_logo
      • pylipid.api.LipidInteraction.dataset
      • pylipid.api.LipidInteraction.residue_list
      • pylipid.api.LipidInteraction.node_list
      • pylipid.api.LipidInteraction.lipid
      • pylipid.api.LipidInteraction.lipid_atoms
      • pylipid.api.LipidInteraction.cutoffs
      • pylipid.api.LipidInteraction.nprot
      • pylipid.api.LipidInteraction.stride
      • pylipid.api.LipidInteraction.dt_traj
      • pylipid.api.LipidInteraction.trajfile_list
      • pylipid.api.LipidInteraction.topfile_list
      • pylipid.api.LipidInteraction.resi_offset
      • pylipid.api.LipidInteraction.save_dir
      • pylipid.api.LipidInteraction.timeunit
      • pylipid.api.LipidInteraction.koff
      • pylipid.api.LipidInteraction.res_time
      • pylipid.api.LipidInteraction.koff_bs
      • pylipid.api.LipidInteraction.res_time_bs
      • pylipid.api.LipidInteraction.residue
      • pylipid.api.LipidInteraction.binding_site
    • pylipid.func
      • pylipid.func.get_node_list
      • pylipid.func.collect_bound_poses
      • pylipid.func.vectorize_poses
      • pylipid.func.calculate_scores
      • pylipid.func.write_bound_poses
      • pylipid.func.analyze_pose_wrapper
      • pylipid.func.calculate_surface_area_wrapper
      • pylipid.func.cluster_DBSCAN
      • pylipid.func.cluster_KMeans
      • pylipid.func.cal_contact_residues
      • pylipid.func.cal_occupancy
      • pylipid.func.cal_lipidcount
      • pylipid.func.Duration
      • pylipid.func.cal_koff
      • pylipid.func.cal_survival_func
      • pylipid.func.calculate_koff_wrapper
    • pylipid.plot
      • pylipid.plot.plot_koff
      • pylipid.plot.plot_residue_data
      • pylipid.plot.plot_residue_data_logo
      • pylipid.plot.plot_binding_site_data
      • pylipid.plot.plot_surface_area
      • pylipid.plot.plot_corrcoef
    • pylipid.util
      • pylipid.util.check_dir
      • pylipid.util.write_PDB
      • pylipid.util.write_pymol_script
      • pylipid.util.sparse_corrcoef
      • pylipid.util.rmsd
      • pylipid.util.get_traj_info
  • Tutorials
    • 0-Application walk thourgh
    • 1-Choose the right distance cutoffs
  • Gallery
  • Demo

GalleryΒΆ

Most representative bound poses

_images/top_ranked_poses.png

Interaction hotspots

_images/surface_hotspots.png

Binding Site analysis

_images/binding_site_comparisons_cutoffs.png

Koff plot

_images/koff_figure.png

Interaction plot

_images/Residence_Time.png

Logo plot

_images/Residence_Time_logo.png

Correlation coefficient

_images/CorrCoef.png

Bound pose RMSD

_images/Pose_RMSD_violinplot.png

Binding site surface

_images/Surface_Area_violinplot.png
Next
Demo
Previous
1-Choose the right distance cutoffs
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