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 | |
TwoBodyContact | ContactBasedPotential | |
P2PScore | ContactBasedPotential | [28] |
StrcGapPenalty | ContactBasedPotential | [29] |
AffineGap | AlignmentEnergy | [30] |
AsaScore | BigMatrixEnergy | [30] |
EnvScore | BigMatrixEnergy | [31] |
GravyScore | BigMatrixEnergy | [32] |
ProbabilisticSecondaryScore | BigMatrixEnergy | [33] |
ProfileScore | BigMatrixEnergy | |
SubstitutionScore | BigMatrixEnergy | [36] |