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

BMC Bioinformatics

Table 1 Potentials implemented within BioShell-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, 24–27]
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]

ISSN: 1471-2105