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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]