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Table 1 Description of scores returned by the primary MQAP methods as well as other local features analyzed in this work.

From: MetaMQAP: A meta-server for the quality assessment of protein models

VERIFY3D

3D-1D profile score for a single residue

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)