Accessible Surface Area (ASA)
Angles
Bturns
Hydrogen Bonds
Quality
Secondary Structure
Stats Explanation
Excluded Volume
Authors, version, copyright notice
Expected Input
Parameter File
Tables
References
PDB file format:
Vadar accepts 20 standard Amino Acids as well as ACE, SME, GLX, ASX, NH2_RES, DEU.
Vadar can not handle other unusual residues!
Table 1. Limits and variation for structural assessment parameters
| High resolution structures | Misfolded structures | |
| Fractional ASA >1.0 | 0.28% | 0.30% |
| Fractional Volume | 0.98±0.11 | 1.0±0.16 |
| Fractional Volume >1.2 | 3.95% | 9.67% |
| Fractional Volume <0.8 | 1.15% | 4.09% |
| Packing Defects | 5.42% | 14.26% |
| Stereo Index | 8.76±0.64 | 7.58±1.48 |
| Stereo Index <7 | 2.6% | 24.33% |
| 3D Profile | 6.32±1.57 | 5.02±2.16 |
| 3D Profile <5 | 15.34% | 46.96% |
| Buried Charges | 1.46% | 3.49% |
| Number of Residues | 2530 | 1003 |
High resolution structures used in Table 1
5PTI 1ERW 4ICB 1F5RI 1EY0 1MXEB 246L 2OVO 1SNM 1RBV 1I0XD 2TRX 1CM2 1FGL 1CM2 1WQQ 1PLC 1HCB 3RN3 1SNC 1A6K
Misfolded structures used in Table 1
1MT2.pdb