SELECTpro takes the amino acid sequence of a protein and the backbone coordinates of
a corresponding model as input and calculates a total pseudo-energy. This value is
normalized to the 0.0 to 1.0 confidence scale. Higher scores indicate higher relative
model confidence.
Individual Energy Terms
The SELECTpro energy function is a linear combination of independently calculated energy terms.
The abbreviations for the energy terms used here are also used in the results email.
Reduced Representation Energy Terms
The following terms are calculated from the backbone plus centroid representation of the protein structure.
PRED-SS_h: Residues predicted as helical by SSpro are penalized if they do not helical in the model.
PRED-SS_s: Residues predicted as beta by SSpro are penalized if they are not beta in the model.
PRED-ACC: Residues predicted as buried by ACCpro are penalized if they are exposed in the model, and residues predicted as exposed are penalized if they are buried.
PRED-CM_fn: Pairs of residues predicted to be in contact by CMAPpro are penalized if they are not in contact in the model.
PRED-CM_fp: Pairs of residues predicted not to be in contact by CMAPpro are penalized if they are in contact in the model.
BETA: Residues of beta-strands predicted by SSpro are penalized if they do not pair with other beta residues.
BB-REP: Repulsive term for explicitly represented atoms in model.
CT-REP: Repulsive term for side-chain centroids.
STAT-ENV: Statistical term for burial/exposure of residue side-chains.
STAT-PW-CI: Context independent statistical term for pairwise interactions.
STAT-PW-CD: Context dependent statistical term for pairwise interactions.
ROG: Models with radius of gyration higher than the value estimated from the sequence length are penalized.
All-Heavy Atom Representation Energy Terms
The following terms are calculated from the all-heavy atom model respresentation.
SC-HB: Side-chain donor and acceptor atoms that are at least partially buried are penalized if they fail to make hydrogen bonds.
LEN-JONES: van der Waals forces with a damped repulsive effect.
SOLVATION: Implicit solvation model.
ELECTRO: Repulsion and attraction of charged groups.
