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. Author manuscript; available in PMC: 2021 May 30.
Published in final edited form as: J Proteomics. 2020 Apr 5;220:103777. doi: 10.1016/j.jprot.2020.103777

Figure 3. Implementations of constrains in the force field.

Figure 3.

(A) Restrictive constraints enforce residues within a given range. (B) Hookean spring potential is a “softer” analog of potential (A). This potential can be approximated by square-well potential function to enable its implementation in DMD. (C) Biasing constraints make it more favorable for residues to be within a certain range. This potential allows constraints to not be satisfied, which is an important property when constraints, representing distinct states, are in conflict with each other. (D) Hybrid constraints potential between that of (B) and (C).