Table 1.
MD simulation conditions for all tested systems
| System | Force field | Solvent | Trajectories | Time (ns) | BMRB Index |
|---|---|---|---|---|---|
| Apo-KID | ff14SB | TIP3P | 5 | 200 | 6784 |
| TIP4P-EW | 5 | 200 | |||
| TIP5P | 5 | 200 | |||
| ff14IDPs | TIP3P | 5 | 200 | ||
| ff14IDPSFF | TIP3P | 5 | 200 | ||
| TIP4P-EW | 5 | 200 | |||
| TIP5P | 5 | 200 | |||
|
| |||||
| Apo-c-Myb | ff14SB | TIP3P | 5 | 130 | - |
| ff14IDPs | TIP3P | 5 | 130 | ||
| ff14IDPSFF | TIP3P | 5 | 130 | ||
| TIP4P-EW | 5 | 130 | |||
| TIP5P | 5 | 130 | |||
|
| |||||
| Apo-Tau | ff14SB | TIP3P | 5 | 100 | 17945 |
| ff14IDPs | TIP3P | 5 | 100 | ||
| ff14IDPSFF | TIP3P | 5 | 100 | ||
| TIP4P-EW | 5 | 100 | |||
| TIP5P | 5 | 100 | |||
|
| |||||
| Apo-IA3 | ff14SB | TIP3P | 5 | 100 | 6078 |
| ff14IDPs | TIP3P | 5 | 100 | ||
| ff14IDPSFF | TIP3P | 5 | 100 | ||
| TIP4P-EW | 5 | 100 | |||
| TIP5P | 5 | 100 | |||
|
| |||||
| Apo-αSynuclein | ff14SB | TIP3P | 5 | 100 | 19337 |
| ff14IDPs | TIP3P | 5 | 100 | ||
| ff14IDPSFF | TIP3P | 5 | 100 | ||
| TIP4P-EW | 5 | 100 | |||
| TIP5P | 5 | 100 | |||
|
| |||||
| Apo-p53 | ff14SB | TIP3P | 5 | 130 | 17760 |
| ff14IDPs | TIP3P | 5 | 130 | ||
| ff14IDPSFF | TIP3P | 5 | 130 | ||
| TIP4P-EW | 5 | 130 | |||
| TIP5P | 5 | 130 | |||
|
| |||||
| Apo-HIVRev | ff14SB | TIP3P | 5 | 140 | 18851 |
| ff14IDPs | TIP3P | 5 | 140 | ||
| CHARMM36m | TIP3P | 5 | 140 | ||
| ff14IDPSFF | TIP3P | 5 | 140 | ||
|
|
|
||||
| TIP4P-EW | 5 | 140 | |||
| TIP5P | 5 | 140 | |||
|
| |||||
| Lysozyme | ff14SB | TIP3P | 5 | 100 | 4562, |
| ff14IDPs | 5 | 100 | |||
| ff14IDPSFF | 5 | 100 | 18304(S2) | ||
|
| |||||
| Ubiquitin | ff14SB | TIP3P | 5 | 100 | 5487, |
| ff14IDPs | 5 | 100 | |||
| ff14IDPSFF | 5 | 100 | 6470(S2) | ||
|
| |||||
| pepK (EGAAKAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||
|
| |||||
| pepL (EGAALAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||
|
| |||||
| pepQ (EGAAQAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||
|
| |||||
| pepG (EGAAGAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||
|
| |||||
| pepT (EGAATAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||
|
| |||||
| pepY (EGAAYAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||
|
| |||||
| pepD (EGAADAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||
|
| |||||
| pepE (EGAAEAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||
|
| |||||
| pepH (EGAAHAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||
|
| |||||
| pepN (EGAANAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||
|
| |||||
| pepI (EGAAIAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||
|
| |||||
| pepP (EGAAPAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||
|
| |||||
| pepV (EGAAVAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||
|
| |||||
| pepW (EGAAWAASS) | ff14SB | TIP3P | 5 | 100 | - |
| ff14IDPSFF | 5 | 100 | |||