ProQ - Protein Quality PredictorProQ 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:
Stand alone version of ProQA 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 modelsYou 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: