ArticleNucleic acids research2011
A coarse-grained force field for Protein-RNA docking.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- CAP: Commutative algebra prediction of protein-nucleic acid binding affinities.Machine learning: science and technology · 2025Article
- Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models.Cell systems · 2025Article
- Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts.PLoS computational biology · 2024Article
- Advances and Challenges in Scoring Functions for RNA-Protein Complex Structure Prediction.Biomolecules · 2024Review
- HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses.BMC bioinformatics · 2024Article
- Conformational variability in proteins bound to single-stranded DNA: A new benchmark for new docking perspectives.Proteins · 2022Article
- Scoring Functions for Protein-RNA Complex Structure Prediction: Advances, Applications, and Future Directions.Communications in information and systems · 2020Article
- A structure-based model for the prediction of protein-RNA binding affinity.RNA (New York, N.Y.) · 2019Article
- Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins.PLoS computational biology · 2019Article
- Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking.Structure (London, England : 1993) · 2019Article
- PredPRBA: Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees.Frontiers in genetics · 2019Article
- An SVM-based method for assessment of transcription factor-DNA complex models.BMC bioinformatics · 2018Article
- 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
- Review
- Determination of an effective scoring function for RNA-RNA interactions with a physics-based double-iterative method.Nucleic acids research · 2018Article
- A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures.PloS one · 2017Article
- Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking.PloS one · 2017Article
- Structure and target interaction of a G-quadruplex RNA-aptamer.RNA biology · 2016Article
- Template-Based Modeling of Protein-RNA Interactions.PLoS computational biology · 2016Article
- Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins.Nucleic acids research · 2016Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The awareness of important biological role played by functional, non coding (nc) RNA has grown tremendously in recent years. To perform their tasks, ncRNA molecules typically unite with protein partners, forming ribonucleoprotein complexes. Structural insight into their architectures can be greatly supplemented by computational docking techniques, as they provide means for the integration and refinement of experimental data that is often limited to fragments of larger assemblies or represents multiple levels of spatial resolution. Here, we present a coarse-grained force field for protein-RNA docking, implemented within the framework of the ATTRACT program. Complex structure prediction is based on energy minimization in rotational and translational degrees of freedom of binding partners, with possible extension to include structural flexibility. The coarse-grained representation allows for fast and efficient systematic docking search without any prior knowledge about complex geometry.
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