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The red vertical lines correspond to identified phase transitions.
| CNA finished for input 1NPC. Results can be downloaded below. | |||||
Files for download: | Input file | Modified input file | |||
Parameters for method type: | Single network - Single structure | No. of FN topologies: - | |||
| Simulation parameters: | # of hydrophobic tethers remains constant during simulation | ||||
| Hydrophobic method: 1 | |||||
| Hydrophobic cutoff: | E-cutoff for H-bonds: | Additional settings: | |||
| Initial value: - | Initial value: -0.1 | Write stability map: No | |||
| Terminal value: - | Terminal value: -6.0 | ||||
| Constant value: 0.25 | Step size: 0.1 | ||||
| Global indices Click here for help | Download raw data | ||||
| a) floppy mode density; b) mean clustersize; rigidity order parameter c) type 1, and d) type 2; cluster configuration entropy, e) type 1, and f) type 2. The red vertical lines correspond to identified phase transitions. | |||||
| a) | | b) | | ||
| c) | | d) | | ||
| e) | | f) | | ||
| Transitions Click here for help | Download raw data | ||||
| Index | Ecut[kcal mol-1] | T[K]* | |||
| Rigidity order parameter type 1 c) | -1.14 | 322.90 | |||
| Rigidity order parameter type 2 d) | -1.14 | 322.90 | |||
| Cluster configuration entropy type 1 e) | -1.14 | 322.90 | |||
| Cluster configuration entropy type 2 f) | -2.55 | 350.99 | |||
| *Temperature conversion taken from eq. 4 in Radestock, S., Gohlke, H. Proteins 2011, 79, 1089-1108. PubMed | |||||
| Local indices Click here for help | Download raw data Download PDB incl. percolation index Download PDB incl. rigidity index | ||
| The lower the percolation index, the longer is a residue part of the giant percolating cluster during thermal unfolding simulation. The lower the rigidity index, the longer is a residue part of a rigid cluster during thermal unfolding simulation. On the right, the respective index is mapped in a color-coded fashion on the protein structure. | |||
 | Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org | ||
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 | Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org |
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| Unfolding nuclei Click here for help | Download raw data Download PDB incl. unfolding nuclei | |
| Unfolding nuclei are weak spots identified in the biomolecule from where the unfolding starts. Residues identified as unfolding nuclei are mapped as red spheres on the protein structure. | ||
Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org | ||