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

In this paper, we report a knowledge-based potential function, named the OPUS-Ca potential, that requires only C alpha positions as input. The contributions from other atomic positions were established from pseudo-positions artificially built from a Ca 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 Ca-based potentials and most other coarse-grained ones that require more information than Ca positions. We hope that this potential function adds a new tool for protein structural modeling.