Advances and Challenges in Scoring Functions for RNA–Protein Complex Structure Prediction
Abstract
:1. Introduction
2. Knowledge-Based Scoring Functions
2.1. Coarse-Grained Knowledge-Based Scoring Functions
2.2. All-Atom Knowledge-Based Scoring Functions
3. Machine-Learning-Based Scoring Functions
4. Benchmarks and Datasets for Assessing Scoring Functions
5. Criteria and Assessment of the Prediction Quality
6. Discussion and Future Directions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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---|---|---|---|---|
Fernández’s potential | 2010 | Pairwise nucleotide–residue propensity | N/A | [63] |
DARS-RNP | 2011 | Decoys as the reference state potential | https://genesilico.pl/software/stand-alone/statistical-potentials (accessed on 29 September 2024) | [36] |
QUASI-RNP | 2011 | Quasi-chemical potential | https://genesilico.pl/software/stand-alone/statistical-potentials (accessed on 29 September 2024) | [36] |
Zacharias’s potential | 2011 | Distance-dependent potential | N/A | [71] |
Wang’s potential | 2012 | Pairwise nucleotide–residue propensity with secondary information | N/A | [72] |
Deck-RP | 2013 | Distance- and environment-dependent potential | http://biophy.hust.edu.cn/new/3dRPC (accessed on 29 September 2024) | [69] |
RPRANK | 2016 | Pairwise nucleotide–residue propensity; RMSD | http://biophy.hust.edu.cn/new/3dRPC (accessed on 29 September 2024) | [70] |
3dRPC-Score | 2017 | Conformations of nucleotide–residue pairs | http://biophy.hust.edu.cn/new/3dRPC (accessed on 29 September 2024) | [37] |
Name | Time | Feature | Availability as a Standalone Method | Reference |
---|---|---|---|---|
Varani’s H-bonding potential | 2004 | Hydrogen-bonding potential | N/A | [11] |
Varani’s all-atom potential | 2007 | Distance-dependent potential | N/A | [76] |
dRNA | 2011 | Volume-fraction corrected distance-scaled, finite, ideal gas reference (DFIRE) energy function | N/A | [12] |
ITScore-PR | 2014 | Pairwise distance-dependent potential; iterative | https://zoulab.dalton.missouri.edu/resources_itscorepr.html (accessed on 29 September 2024) | [22] |
DITScore-PR | 2019 | Pairwise distance-dependent potential; double-iterative | http://huanglab.phys.hust.edu.cn/mprdock/ (accessed on 29 September 2024) | [31] |
Name | Time | Representation | Feature | Availability as a Standalone Method | Reference |
---|---|---|---|---|---|
Parisien’s potential | 2013 | Coarse-grained | Chemical context profiles | N/A | [89] |
DRPScore | 2023 | All-atom | Convolutional neural network | https://github.com/Zhaolab-GitHub/DRPScore_v1.0 (accessed on 29 September 2024) | [23] |
Benchmark | Development | Time | Total Number of Cases | Number of Cases | Availability | |||||
---|---|---|---|---|---|---|---|---|---|---|
Bound–Unbound | Unbound–Unbound | Easy | Medium | Difficult | Reference | |||||
Benchmark I | Zou group | 2013 | 72 | 20 | 52 | 49 | 16 | 7 | [95] | https://zoulab.dalton.missouri.edu/RNAbenchmark/index.htm (accessed on 29 September 2024) |
Benchmark II | Fernández-Recio group | 2012 | 106 * | 62 | 9 | 64 | 24 | 18 | [93] | https://life.bsc.es/pid/protein-rna-benchmark/ (accessed on 29 September 2024) |
Benchmark III | Bahadur group | 2012/2016 | 126 | 105 | 21 | 72 | 25 | 19 | [92,94] | N/A |
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Zeng, C.; Zhuo, C.; Gao, J.; Liu, H.; Zhao, Y. Advances and Challenges in Scoring Functions for RNA–Protein Complex Structure Prediction. Biomolecules 2024, 14, 1245. https://doi.org/10.3390/biom14101245
Zeng C, Zhuo C, Gao J, Liu H, Zhao Y. Advances and Challenges in Scoring Functions for RNA–Protein Complex Structure Prediction. Biomolecules. 2024; 14(10):1245. https://doi.org/10.3390/biom14101245
Chicago/Turabian StyleZeng, Chengwei, Chen Zhuo, Jiaming Gao, Haoquan Liu, and Yunjie Zhao. 2024. "Advances and Challenges in Scoring Functions for RNA–Protein Complex Structure Prediction" Biomolecules 14, no. 10: 1245. https://doi.org/10.3390/biom14101245
APA StyleZeng, C., Zhuo, C., Gao, J., Liu, H., & Zhao, Y. (2024). Advances and Challenges in Scoring Functions for RNA–Protein Complex Structure Prediction. Biomolecules, 14(10), 1245. https://doi.org/10.3390/biom14101245