OPUS-Ca: a knowledge-based potential function requiring only Calpha positions.
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.
Wu
Yinghao
Y
Department of Bioengineering, Rice University, Houston, TX 77005, USA.
Lu
Mingyang
M
Chen
Mingzhi
M
Li
Jialin
J
Ma
Jianpeng
J
D000465:Algorithms; D006860:Hydrogen Bonding; D051188:Knowledge Bases; D008956:Models, Chemical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins