Instead, it uses substitution matrix, secondary structure prediction, and contact capacity potentials to thread a sequence throught the set of structures. Secondary structure prediction is made with the Nearest Neighbor method by A.Salamov and V.Solovyev . 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. The program 123D is written by Nickolai Alexandrov in close collaboration with Ralf Zimmer and V.Solovyev .