Also, a library of HMMs built by similar methods from PDB sequences is used to score the target sequence. The current version of this server uses a fold library, which is automatically updated every week. It uses predicted versus observed secondary structure and sequence profiles for both the target and for the folds in the library. The evaluated results are taken from the consensus prediction only. Contact capacity potentials reflect mainly hydrophobicity of the amino acids.
Hydrophobicity is the major driving force for protein folding.
Without pairwise contact potentials we can use a simple and fast dynamic programming algorithm to align a sequence with a structure.