Figure 4

EvP and REP derivation protocols. (a) The REP potential was built in a three-step process to: step 1, generate a non-redundant set of protein structures from the PDB database; step 2, calculate all residue-residue distance frequencies within each of the representative chains from step 1; and step 3, derive a knowledge-based potential using the inverse Boltzmann law to transform the raw frequencies into pseudo-energy terms. (b) The EvPs were built in a six-step process to: step 1, generate a non-redundant set of protein structures from the PDB database; step 2, select each of the representative chains as query structures; step 3, calculate a MSA using the PSI-BLAST program; step 4, thread all homologous sequences into the query structure using the sequence-based alignment from the previous step; step 5, calculate all residue-residue distance frequencies; and step 6, derive a knowledge-based potential using the inverse Boltzmann law to transform the raw frequencies into pseudo-energy terms.