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Protein Science (2007), 16:1449-1463. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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OPUS-Ca: A knowledge-based potential function requiring only C{alpha} positions

Yinghao Wu1,4, Mingyang Lu2,4, Mingzhi Chen3, Jialin Li3, and Jianpeng Ma1,2,3

1 Department of Bioengineering, Rice University, Houston, Texas 77005, USA
2 Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
3 Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA

(RECEIVED January 28, 2007; FINAL REVISION April 14, 2007; ACCEPTED April 16, 2007)

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 C{alpha} 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 C{alpha}-based potentials and most other coarse-grained ones that require more information than C{alpha} positions. We hope that this potential function adds a new tool for protein structural modeling.

Keywords: knowledge-based potential function; decoy recognition; structure prediction; protein folding


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Copyright © 2007 by The Protein Society.