Hydrogen-bond persistence
Which protein-ligand hydrogen bonds hold through a Molecular dynamics trajectory, and for how much of it — whether a bound complex is stable at the interface.
Hydrogen-bond persistence
What it does
Takes a Molecular dynamics trajectory that included a bound ligand, and reports which hydrogen bonds between the protein and the ligand actually held over the course of the simulation, and for what fraction of it. A structure can look stable overall (see Trajectory stability) while the specific contacts holding a ligand in place come and go, or never form at all — this tool answers that more specific question.
How persistence is measured
For every frame of the trajectory, this tool checks every possible hydrogen bond between the protein and the ligand against standard distance and angle criteria. A bond that satisfies those criteria in a given frame counts as present in that frame; persistence is the fraction of frames a given donor–acceptor pair was present in.
Reading the output
The table lists every distinct contact found, ranked by how persistent it was — a bond present in 90% of frames is a genuinely stable interaction; one present in 5% is a fleeting, likely incidental contact. Zero contacts is a real, meaningful result, not an error — it means the simulation found no stable hydrogen-bonding interface at all between the protein and the ligand, which is exactly what happens when a ligand starts the simulation in an arbitrary position rather than a properly docked pose (see limitations).
Input
A trajectory and its reference structure from a Molecular dynamics run that included a ligand — the same pairing Trajectory stability takes. A trajectory from a protein-only run (no ligand) can't be analyzed here.
Important limitations
Only meaningful for a properly docked starting pose. Molecular dynamics places a supplied ligand near the protein without docking it — if the ligand you gave it wasn't already docked (e.g. with Small-molecule docking) before the simulation ran, this tool will correctly report little to no persistent contact, because there was no real bound pose for hydrogen bonds to hold onto in the first place. That result reflects the input, not a limitation of the analysis itself.
Protein–ligand contacts only. This doesn't report protein-internal or water-mediated hydrogen bonds — it answers the specific question of whether the ligand stayed hydrogen-bonded to the protein.