Abstract
In this paper, we report a knowledge-based potential function, named the OPUS-Ca potential, that requires only Cα positions as input. The contributions from other atomic positions were established from pseudo-positions artificially built from a Cα 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 Cα-based potentials and most other coarse-grained ones that require more information than Cα positions. We hope that this potential function adds a new tool for protein structural modeling. Published by Cold Spring Harbor Laboratory Press.
Original language | English (US) |
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Pages (from-to) | 1449-1463 |
Number of pages | 15 |
Journal | Protein Science |
Volume | 16 |
Issue number | 7 |
DOIs | |
State | Published - Jul 2007 |
Externally published | Yes |
Keywords
- Decoy recognition
- Knowledge-based potential function
- Protein folding
- Structure prediction
ASJC Scopus subject areas
- Biochemistry
- Molecular Biology