dorsal/arxiv
View SchemaUnbound Protein-Protein Docking Selections by the DFIRE-based Statistical Pair Potential
| Authors | Song Liu, Chi Zhang, Yaoqi Zhou |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0406025 |
| URL | https://arxiv.org/abs/q-bio/0406025 |
Abstract
A newly developed statistical pair potential based on Distance-scaled Finite Ideal-gas REference (DFIRE) state is applied to unbound protein-protein docking structure selections. The performance of the DFIRE energy function is compared to those of the well-established ZDOCK energy scores and RosettaDock energy function using the comprehensive decoy sets generated by ZDOCK and RosettaDock. Despite significant difference in the functional forms and complexities of the three energy scores, the differences in overall performance for docking structure selections are small between DFIRE and ZDOCK2.3 and between DFIRE and RosettaDock. This result is remarkable considering that a single-term DFIRE energy function was originally designed for monomer proteins while multiple-term energy functions of ZDOCK and RosettaDock were specifically optimized for docking. This provides hope that the accuracy of the existing energy functions for docking can be improved.
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"abstract": "A newly developed statistical pair potential based on Distance-scaled Finite\nIdeal-gas REference (DFIRE) state is applied to unbound protein-protein docking\nstructure selections. The performance of the DFIRE energy function is compared\nto those of the well-established ZDOCK energy scores and RosettaDock energy\nfunction using the comprehensive decoy sets generated by ZDOCK and RosettaDock.\nDespite significant difference in the functional forms and complexities of the\nthree energy scores, the differences in overall performance for docking\nstructure selections are small between DFIRE and ZDOCK2.3 and between DFIRE and\nRosettaDock. This result is remarkable considering that a single-term DFIRE\nenergy function was originally designed for monomer proteins while\nmultiple-term energy functions of ZDOCK and RosettaDock were specifically\noptimized for docking. This provides hope that the accuracy of the existing\nenergy functions for docking can be improved.",
"arxiv_id": "q-bio/0406025",
"authors": [
"Song Liu",
"Chi Zhang",
"Yaoqi Zhou"
],
"categories": [
"q-bio.BM",
"q-bio.QM"
],
"title": "Unbound Protein-Protein Docking Selections by the DFIRE-based Statistical Pair Potential",
"url": "https://arxiv.org/abs/q-bio/0406025"
},
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