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Table 1 Potentials implemented within BioShell-threading

From: BioShell-Threading: versatile Monte Carlo package for protein 3D threading

Score type

Description

AlignemntEnergy

Base class for all alignment scores

ByAtomEnergy

Score depends solely on a single position in a target and the aligned position in a template

StructureBasedScore

Knows about target and template atomic coordinates

BigMatrixEnergy

Pairwise per-position energy may be pre-calculated and stored in a 2D array

ContactBasedEnergy

Energy that depends on a template contact map

PairwiseContactEnergy

Contact based energy that is pairwise-decomposable, but can’t be precalculated (otherwise it would result in BigMatrixEnergy score)

Score name

Derived from

References

DaliScore

StructureBasedScore

[20]

RMSDAlignScore

StructureBasedScore

[21]

TMAlignScore

StructureBasedScore

[17]

GoLikeScore

ContactBased Potential

[22, 23]

TwoBodyContact

ContactBasedPotential

[18, 19, 2427]

P2PScore

ContactBasedPotential

[28]

StrcGapPenalty

ContactBasedPotential

[29]

AffineGap

AlignmentEnergy

[30]

AsaScore

BigMatrixEnergy

[30]

EnvScore

BigMatrixEnergy

[31]

GravyScore

BigMatrixEnergy

[32]

ProbabilisticSecondaryScore

BigMatrixEnergy

[33]

ProfileScore

BigMatrixEnergy

[34, 35]

SubstitutionScore

BigMatrixEnergy

[36]