From: MetaMQAP: A meta-server for the quality assessment of protein models
VERIFY3D | 3D-1D profile score for a single residue |
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VERIFY3Dw5 | VERIFY3D score averaged over a 5 residue window |
PROSApair | pair energy (atom-atom interactions) |
PROSAsurf | surface energy (atom-solvent interactions) |
PROSA | combination of PROSApair and PROSAsurf |
ANOLEA | distance – dependent empirical potential. It evaluates the non-local environment (NLE) of each heavy atom in the model |
ANOLEAw5 | ANOLEA score averaged over a 5 residue window |
PROVE | average relative volume for all atoms of a residue |
BALA | mean of a four-body statistical potential, applied to tetrahedral quadruplets or spatially neighbouring residues |
REFINERloc | pseudoenergy of local contacts |
REFINERnonloc | pseudoenergy of long-distance contacts |
REFINERhydro | pseudoenergy of H-H bond interaction |
REFINERbur | pseudoenergy of burial |
REFINER | weighted sum of all REFINER pseudoenergies |
TUNE | score based on neural network that predict local quality of residue from both a local and non local contact of residues in the mode |
FractionPolar | fraction of non-polar residues in area of given residue (ENVIRONMENT) |
BuriedArea | burial of the residue (ENVIRONMENT) |
LocalNeighbours | number of residues within the distance of 10 Ã… in space and within 8 residues in the sequence |
NonLocalNeighbours | number of residues within the distance of 10 Ã… in space and more distant than 8 residues in the sequence. |
ResDepth | the distance between the C-α atom of a residue and the closest geometrically plausible position of a water molecule on the surface of the protein |
PROQ | It 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 |
PROQRES | score based on neural network which estimate local structure from: atom-atom contacts, residue-residue contacts, secondary structure context, and solvent accessibility |
AbsAccessibility | absolute value of solvent accessibility for all atom off a residue (according to NACCESS) |
RelAccessibility | proportion of absolute solvent accessibility of a given residue to the solvent accessibility of the same type of residue (X) in a model tripeptyde Ala-X-Ala (according to NACCESS) |
LoopProb | probability of a loop conformation in secondary structure predicted by PSIPRED |
HelixProb | probability of a helical conformation in secondary structure predicted by PSIPRED |
StrandProb | probability of an extended conformation in secondary structure predicted by PSIPRED |
SSAgreement | agreement between secondary structure predicted by PSIPRED and secondary structure observed in the model (calculated by DSSP) |