OPUS‐Ca: A knowledge‐based potential function requiring only Cα positions

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Abstract
In this paper, we report a knowledge‐based potential function, named the OPUS‐Ca potential, that requires only Cα positions as input. The contributions from other atomic positions were established from pseudo‐positions artificially built from a Cα trace for auxiliary purposes. The potential function is formed based on seven major representative molecular interactions in proteins: distance‐dependent pairwise energy with orientational preference, hydrogen bonding energy, short‐range energy, packing energy, tri‐peptide packing energy, three‐body energy, and solvation energy. From the testing of decoy recognition on a number of commonly used decoy sets, it is shown that the new potential function outperforms all known Cα‐based potentials and most other coarse‐grained ones that require more information than Cα positions. We hope that this potential function adds a new tool for protein structural modeling.