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Table 1 Brief description of six reference states for distance-dependent atom-pair potential

From: Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction

Reference statea Description
Averaging (ave-) Take the average distance distribution over different atom types from experimental conformations as the reference state, which means the distance distributions for all types of atom pair are identical in the reference state [25].
Quasi-chemical approximation (kbp-) Use the overall distance distribution of atom pair from experimental structures and calculate the specific distance distribution of atom types i and j based on the mole fraction (on the whole dataset) of atom type i and j [26].
Finite ideal-gas (dfire-) Treat the reference state as finite ideal-gas that probability of atom pair in a particular distance bin increases in ra with a to-be-determined constant a (a < 2) [27].
Spherical non-interacting (dope-) Treat the reference state as a sphere in which all atoms of a protein evenly distributed without ineraction. The size of sphere is specifically decided by corresponding experimental structure [9].
Random-walk chain (rw-) Treat the reference state as an ideal random-walk chain of a rigid step length, which mimics well the generic entropic elasticity and inherent connectivity of polymer protein molecules and yet ignores the atomic interactions of amino acids [29].
Atom-shuffled (srs-) Generate a shuffled structure dataset by preserving all atomic positions while shuffling atom identities within each of the experimental structures [28].
  1. aThe abbreviation is given in parentheses