Viewer elements:

• Sequence: Amino acids sequence of the protein chain (SEQRES records). Missing residues are highlighted in grey and PDB author numbering is available in the hover tooltip.
• Secondary structure: DSSP secondary structure assignment (3 states) of the 1^st frame of the molecular dynamics simulation.
• Chain interactions: Residues interacting with another co-crystallized protein chain. An interaction is defined if the distance between the α-carbon of the residue of interest and any heavy-atom of the co-crystallized residue is inferior to 6 Å.
• Ligands interactions: Residues interacting with co-crystallized ligands. (α-carbon / ligand heavy-atom distance inferior to 6 Å.)
• Ions interactions: Residues interacting with co-crystallized ions. (α-carbon / ion distance inferior to 6 Å.)
• Nucleotides interactions: Residues interacting with co-crystallized nucleotides. (α-carbon / nucleotide heavy-atom distance inferior to 6 Å.)
• ECOD: ECOD domain(s) delineation(s). Non-redndant domains are coloured in dark blue, and redndant ones in light blue.
• CATH: CATH domain(s) delineation(s).
• SCOPe: SCOPe domain(s) delineation(s).
• SWORD: SWORD2 domain(s) delineation(s) assigned on 1st MD frame.
• B-factor: Experimental B-factor values of α-carbons. For the visualisation, unknown B-factors values (missing residues) are set to max (Norm. val = 1).
• Avg. RMSF: Averaged RMSF over the 3 replicates. Average ± SD values are visible in the hover tooltip.
• Avg. Neq: Averaged Neq over the 3 replicates. Average ± SD values are visible in the hover tooltip.
• AF2 pLDDT: AlphaFold2 pLDDT (inverted for visualisation). pLDDT is the per-residue prediction confidence metric, not a flexibility measurement.

• Normalisation by protein: Normalisation between the min and max of the queried protein, and are represented in linear scale.
• Global normalisations: Normalisation between the min and the max of the entire database. This allows us to compare the flexibility differences between different proteins. To facilitate the visualisation, values are represented in log2 scale.

This panel allows us to compare the flexibility (B-factor, RMSF, Neq), stability (RMSD, gyration radius) and AlphaFold2 prediction confidence (pLDDT) of the 3 molecular dynamics replicates.

Metrics:

• B-factor: Experimental B-factor values of α-carbons (in Ų). Unknown B-factors values (missing residues) are not displayed.
• RMSF: RMSF values of the 3 replicates (in Å).
• Neq: Neq values of the 3 replicates.
• pLDDT: AlphaFold2 pLDDT. pLDDT is the per-residue prediction confidence metric, not a flexibility measurement.

Metric:

• RMSD: RMSD values of the 3 replicates in Å.

Metric:

• Gyration radius: Gyration radius values of the 3 replicates in Å.

Representation:

• Contact map frequency: Frequency of contact along the trajectory. A high frequency (in blue) corresponds to a contact conserved during the simulation and conversely a low frequency (white) to a contact rarely observed in the trajectory.
• Contact map animation: Raw contact assignment for each frame of the dynamics (no contact/0 or contact/1).

To improve the readability, users can click and drag on a region of the plot to zoom-in, and double-click to zoom-out. Moreover, contact frequencies values can be seen in the hover tooltip of each residue pair.

Representations:

• Total Ramachandran plot: Overlap of the dihedral angles values of all the residues for every nanoseconds of the dynamics.
• Animated Ramachandran plot: Animated Ramachandran plot of all the residues with a 1ns step. This plot allows us to follow the variation of dihedral angles of the residues along the trajectory.
• Glycine Ramachandran plot: Overlap of the dihedral angles values of the glycine residues for every nanoseconds of the dynamics.
• Proline Ramachandran plot: Overlap of the dihedral angles values of the proline residues for every nanoseconds of the dynamics.
• Pre-proline Ramachandran plot: Overlap of the dihedral angles values of the pre-proline residues for every nanoseconds of the dynamics.

The static Ramachandran plots residues are coloured by density, from blue (low density) to red (high density).

The dynamic Ramachandran plot residues are coloured by position in the sequence, from blue (N-ter) to red (C-ter).

• Flexibility descriptors:
  • RMSF: RMSF (in Å) of the replicate
  • B-factor: Experimental B-factor (in Ų)
  • Neq: Neq of the replicate
  • pLDDT: AlphaFold2 pLDDT (inverted for visualisation). pLDDT is the per-residue prediction confidence metric, not a flexibility measurement.
The thickness and the colour of the protein structure are proportional to the represented metric. A small flexibility value will thus be represented by a small blue worm, and a big value by a big red worm.

• General descriptors:
  • Monochrome: Colour the protein in light blue
  • Sequence position: Colour the residues according to their position in the sequence. The start (N-ter) of the protein will therefore be in blue, and the end (C-ter) in red.
  • Secondary structure: Colour the protein based on its secondary structure assignment (DSSP). α-helix are displayed in red, β-sheet are in yellow, and loops are in white.
The protein structure is represented in cartoon, showing the secondary structures.

Dynamics: Visualise the trajectory of the molecular dynamics

To launch the molecular dynamics animation, click on , then on Start.

• Visualisation characteristics
  • Number of frames: 100
  • Step time: 1 ns
See About for details on the complete molecular dynamics parameters used.