ArticlePloS one2017
A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Inferring the qualities of protein-RNA models with graph transformers.Bioinformatics (Oxford, England) · 2026Article
- Advances and Challenges in Scoring Functions for RNA-Protein Complex Structure Prediction.Biomolecules · 2024Review
- Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure.Interdisciplinary sciences, computational life sciences · 2024Review
- HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses.BMC bioinformatics · 2024Article
- Evaluating native-like structures of RNA-protein complexes through the deep learning method.Nature communications · 2023Article
- Long non-coding RNA AC122108.1 promotes lung adenocarcinoma brain metastasis and progression through the Wnt/β-catenin pathway by directly binding to aldolase A.Annals of translational medicine · 2021Article
- HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study.Briefings in bioinformatics · 2021Article
- Biophysical and Dynamic Characterization of Fine-Tuned Binding of the Human Respiratory Syncytial Virus M2-1 Core Domain to Long RNAs.Journal of virology · 2020Article
- Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes.RNA (New York, N.Y.) · 2018Article
- Determination of an effective scoring function for RNA-RNA interactions with a physics-based double-iterative method.Nucleic acids research · 2018Article
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Authors and funding
3 authors.
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Abstract
Computational prediction of RNA-protein complex 3D structures includes two basic steps: one is sampling possible structures and another is scoring the sampled structures to pick out the correct one. At present, constructing accurate scoring functions is still not well solved and the performances of the scoring functions usually depend on used benchmarks. Here we propose a pair-conformation-dependent scoring function, 3dRPC-Score, for 3D RNA-protein complex structure prediction by considering the nucleotide-residue pairs having the same energy if their conformations are similar, instead of the distance-only dependence of the most existing scoring functions. Benchmarking shows that 3dRPC-Score has a consistent performance in three test sets.
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