ProQ - Protein Quality Predictor
ProQ is a neural network based predictor that based on a number of
structural features predicts the quality of a protein model. ProQ is
optimized to find correct models in contrast to other methods which
are optimized to find native structures. Two quality measures are
predicited LGscore and MaxSub.
LGscore is -log of a P-value and MaxSub ranges from 0-1, were 0 is
insignificant and 1 very significant.
Different ranges of quality:
Correct
LGscore > 1.5
MaxSub > 0.1
|
Good
LGscore > 3
MaxSub > 0.5
|
Very good
LGscore > 5
MaxSub > 0.8
|
Stand alone version of ProQ
A stand alone version of ProQ for linux can be download here.
Before running the program please see the instructions in the README.
Build all-atom models
You can build all-atom models from alignment on a known structure here. To use
it you need an academic license of MODELLER. The necessary key can be
obtained here. The
model is automatically evalutated using ProQ. The scores are supplied
in the header of the model as:
REMARK PROQ-LG 0.588
REMARK PROQ-MX 0.003
Additional
tables to the ProQ paper.
Results for the different methods for each protein on known Decoy Sets and on models created
from LiveBench-2. All
atom models from LiveBench-2 can be downloaded here (205MB). Each
file has the MaxSub, LGscore, RMSD and when ever possible also the
Pcons score in the header.
For each method the
following tables is presented:
| Protein |
decoys |
rank |
MX |
LG |
RMSD |
Z |
Z-nat |
| 4state_reduced |
|
|
|
|
|
|
|
| 1ctf |
630 |
1 |
1.00 |
4.11 |
0.00 |
2.7 |
5.1 |
| 1r69 |
675 |
2 |
0.82 |
2.80 |
1.66 |
3.4 |
6.2 |
| 1sn3 |
660 |
1 |
1.00 |
3.99 |
0.00 |
1.9 |
4.6 |
| 2cro |
674 |
1 |
1.00 |
3.99 |
0.00 |
2.0 |
4.8 |
| Protein |
|
name of target protein |
| decoys |
|
number of decoys in the set |
| rank |
|
rank of the native structure |
| MX |
|
MaxSub for the highest ranked model |
| LG |
|
LGscore for the highest ranked model |
| RMSD |
|
RMSD for the highest ranked model |
| Z |
|
Z-score for seperating incorrect and correct models |
| Z-nat |
|
Z-score for the native structure |
| 
