Contact-dependent potential

We designed contact-dependent potential (CDP). Two residues, with sequence separation equal to or larger than 6, are considered to be in-contact if their Euclidean distance is less than 9 Å in the 3D space. Therefore, the M, f_reference, and f_observed for the CDP for any two residues (each represented by their Cα or Cβ atom and each belonging to 20 residue-type classes c_j) being in-contact are defined as:

For the ith and jth residues (represented by Cα or Cβ atoms) with residue type R_i and c_j, suppose they have a specific class combination (ss, c_j), we define  f_i(ss, c_j) as the number of occurrences of that combination of states for residue type R_i (one occurrence number is generated for a residue type, with in total 20 occurrence numbers generated for 20 amino acid types).