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.

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@article{Wu2007OPUSCaAK, title={OPUS-Ca: a knowledge-based potential function requiring only Calpha positions.}, author={Yinghao Wu and Mingyang Lu and Mingzhi Chen and Jialin Li and Jianpeng Ma}, journal={Protein science : a publication of the Protein Society}, year={2007}, volume={16 7}, pages={1449-63} }