OPUS-Ca: a knowledge-based potential function requiring only Calpha positions |
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Authors: | Wu Yinghao Lu Mingyang Chen Mingzhi Li Jialin Ma Jianpeng |
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Institution: | Department of Bioengineering, Rice University, Houston, TX 77005, USA. |
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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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Keywords: | knowledge-based potential function decoy recognition structure prediction protein folding |
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