Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes

Fu Chen, Huiyong Sun, Junmei Wang, Feng Zhu, Hui Liu, Zhe Wang, Tailong Lei, Youyong Li, Tingjun Hou

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Molecular docking provides a computationally efficient way to predict the atomic structural details of protein-RNA interactions (PRI), but accurate prediction of the three-dimensional structures and binding affinities for PRI is still notoriously difficult, partly due to the unreliability of the existing scoring functions for PRI. MM/PBSA and MM/GBSA are more theoretically rigorous than most scoring functions for protein-RNA docking, but their prediction performance for protein-RNA systems remains unclear. Here, we systemically evaluated the capability of MM/PBSA and MM/GBSA to predict the binding affinities and recognize the near-native binding structures for protein-RNA systems with different solvent models and interior dielectric constants (εin). For predicting the binding affinities, the predictions given by MM/GBSA based on the minimized structures in explicit solvent and the GBGBn1 model with εin = 2 yielded the highest correlation with the experimental data. Moreover, the MM/GBSA calculations based on the minimized structures in implicit solvent and the GBGBn1 model distinguished the near-native binding structures within the top 10 decoys for 117 out of the 148 protein-RNA systems (79.1%). This performance is better than all docking scoring functions studied here. Therefore, the MM/GBSA rescoring is an efficient way to improve the prediction capability of scoring functions for protein-RNA systems.

Original languageEnglish (US)
Pages (from-to)1183-1194
Number of pages12
JournalRNA
Volume24
Issue number9
DOIs
StatePublished - Sep 1 2018
Externally publishedYes

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RNA
Proteins
RNA-Binding Proteins
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Keywords

  • Binding free energy
  • Docking
  • MM/GBSA
  • MM/PBSA
  • Protein-RNA interactions

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes. / Chen, Fu; Sun, Huiyong; Wang, Junmei; Zhu, Feng; Liu, Hui; Wang, Zhe; Lei, Tailong; Li, Youyong; Hou, Tingjun.

In: RNA, Vol. 24, No. 9, 01.09.2018, p. 1183-1194.

Research output: Contribution to journalArticle

Chen, Fu ; Sun, Huiyong ; Wang, Junmei ; Zhu, Feng ; Liu, Hui ; Wang, Zhe ; Lei, Tailong ; Li, Youyong ; Hou, Tingjun. / Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes. In: RNA. 2018 ; Vol. 24, No. 9. pp. 1183-1194.
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