FlexAppeal
lysozyme_benzene_100ns
- Simulated
- 100ns
- Frames
- 10,000
500 packed for viewing
- Final RMSD
- 0.95Å
mean of the last 10% of frames
- Radius of gyration
- 16.63Å
trajectory mean
- Hydrogen bonds
- 308
occupancy > 10%
- Helix content
- 62%
trajectory mean
- Throughput
- 298ns/day
OpenCL
- Wall time
- 8.1h
- Settles after
- 0.5ns
1% of production, by pymbar.detect_equilibration
- Force field
- amber14-all.xml
- Platform
- OpenCL
- Structure
- 181l.pdb
Structure
The decimated trajectory, 500 frames of 2615 atoms. Press play, or scrub the frame slider: the plots below highlight the frame you are on.
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The binding site
| Pose | 100.0 | 32% | |
|---|---|---|---|
| Occupancy | 100.0 | 21% | |
| Interactions | 100.0 | 21% | |
| Energy -9.9 kcal/mol ± 6.6 | 16.5 | 16% | |
| Convergence | 100.0 | 10% | |
| Conformation | the ligand has no rotatable bond | — |
|
Ligand pose
What this shows
Two fits of the same ligand. Against the pocket, the curve is the ligand moving in a receptor held still; against itself, it is the ligand changing shape. The shaded head is the equilibration that was measured and not scored.
Centroid drift
What this shows
Displacement of the ligand centroid from where it started. The dotted line at 5 Å is the drift beyond which DeepFlex caps a grade.
Pocket occupancy
What this shows
Receptor residues in contact with the ligand. The dotted line is a quarter of the contacts present at the start, which is the threshold for counting a frame as still bound.
Interaction occupancy
What this shows
Which contacts carried the pose, and for how much of the scored window. Typed from heavy-atom geometry, so these are polar, ionic and hydrophobic contacts rather than a full interaction fingerprint.
Contact barcode
What this shows
When each contact was present, busiest first. Gaps are the contact breaking and reforming.
Pose clusters
What this shows
How the scored window divides into distinct poses. One tall bar near zero is a ligand that held its pose.
Ligand atom fluctuation
What this shows
Which part of the ligand moves, about its own mean position.
Receptor flexibility
What this shows
Per-residue backbone fluctuation, with the binding-site residues marked. A mobile pocket makes every pose measurement noisier.
Frame-to-frame RMSD
What this shows
Every frame against every other. Blocks along the diagonal are distinct states; a uniform field is a run that stayed in one.
Residue cross-correlation
What this shows
Which parts of the receptor move together. Blue is correlated, red is anticorrelated.
MM/GBSA, term by term
What this shows
Where the binding energy comes from. The bars are the difference block, complex minus receptor minus ligand, which is the only part of an MM/GBSA calculation that is a binding quantity. Error bars are the standard deviation over the sampled frames, not the standard error. igb=2, single trajectory, no entropy term: good for ranking ligands against each other, not an affinity.
The whole system
RMSD
What this shows
How far the structure has moved from its reference. A plateau means the trajectory has settled; a steady climb means it has not.
Radius of gyration
What this shows
Global compactness. A rise suggests unfolding or expansion.
Per-residue fluctuation
What this shows
Which parts of the molecule move. Peaks are usually loops and termini.
Solvent exposure
What this shows
Total solvent-accessible surface area over time.
Secondary structure content
What this shows
Helix and sheet content over the trajectory.
Secondary structure timeline
What this shows
Per-residue assignment at every frame. Vertical stripes are transient melting; horizontal bands are stable elements.
Contact map
What this shows
How often each residue pair is in contact across the whole trajectory.
Essential dynamics
What this shows
The two dominant collective motions, with each frame coloured by time. Distinct clouds mean distinct conformational states.
Conformational clusters
What this shows
Representative states found by RMSD clustering.
Convergence
What this shows
Each measure on its own axis. Energies, temperature and density differ by orders of magnitude, so sharing a plot between any two of them would make their alignment arbitrary and any apparent correlation fictional.