title: OPUS-Ca: a knowledge-based potential function requiring only Calpha positions.
abstract: In this paper, we report a knowledge-based potential function, named the OPUS-Ca potential, that requires only Calpha positions as input. The contributions from other atomic positions were established from pseudo-positions artificially built from a Calpha 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 Calpha-based potentials and most other coarse-grained ones that require more information than Calpha positions. We hope that this potential function adds a new tool for protein structural modeling.
authors.affiliation: Department of Bioengineering, Rice University, Houston, TX 77005, USA.
authors.forename: Yinghao
authors.initials: Y
authors.lastname: Wu
authors.forename: Mingyang
authors.initials: M
authors.lastname: Lu
authors.forename: Mingzhi
authors.initials: M
authors.lastname: Chen
authors.forename: Jialin
authors.initials: J
authors.lastname: Li
authors.forename: Jianpeng
authors.initials: J
authors.lastname: Ma
mesh_terms: D000465:Algorithms; D006860:Hydrogen Bonding; D051188:Knowledge Bases; D008956:Models, Chemical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins