Software:Model Quality Assessment General Description
From Honiglab_public
Global and Local Quality Assessment of Protein Models
Both methods combine a number of state-of-the-art statistical potentials and scoring functions using support vector machines (SVMs). The statistical potentials used here include solvation potentials, environmental potentials, pairwise potentials, hydrogen bonding potentials and backbone dihedral potentials. The scoring functions used here include two tabulated physical functions that were derived from the OPLS united-atom force field and three functions that primarily compare secondary structure assignment by DSSP and secondary structure prediction by PSIPRED. The global quality measures being predicted here include C-alpha RMSD (CARMS), C-alpha RMSD of secondary structure elements (SSRMS), GDT_TS, MaxSub and TM-score. The local quality being predicted here is the so-called S-score proposed by Wallner and Elofsson (Protein Sci. 2006). A window of 11 residues is used to evaluate the local quality of the center residue. A large number of models have been compiled from CASP5, CASP6 and CASP7 for the SVM training and testing. More methodological details can be found in the upcoming paper by Zhu and Honig (in preparation).
Model Quality Assessment Program is supported by a funding from the NIH Grant # GM30518
Developed in the Honig Lab
