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PRIME-3D2D is a 3D2D model to predict binding sites of protein-RNA interaction.

ABSTRACT: Protein-RNA interaction participates in many biological processes. So, studying protein-RNA interaction can help us to understand the function of protein and RNA. Although the protein-RNA 3D3D model, like PRIME, was useful in building 3D structural complexes, it can't be used genome-wide, due to lacking RNA 3D structures. To take full advantage of RNA secondary structures revealed from high-throughput sequencing, we present PRIME-3D2D to predict binding sites of protein-RNA interaction. PRIME-3D2D is almost as good as PRIME at modeling protein-RNA complexes. PRIME-3D2D can be used to predict binding sites on PDB data (MCC?=?0.75/0.70 for binding sites in protein/RNA) and transcription-wide (MCC?=?0.285 for binding sites in RNA). Testing on PDB and yeast transcription-wide data show that PRIME-3D2D performs better than other binding sites predictor. So, PRIME-3D2D can be used to predict the binding sites both on PDB and genome-wide, and it's freely available.

SUBMITTER: Xie J

PROVIDER: S-EPMC7366699 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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PRIME-3D2D is a 3D2D model to predict binding sites of protein-RNA interaction.

Xie Juan J Zheng Jinfang J Hong Xu X Tong Xiaoxue X Liu Shiyong S

Communications biology 20200716 1

Protein-RNA interaction participates in many biological processes. So, studying protein-RNA interaction can help us to understand the function of protein and RNA. Although the protein-RNA 3D3D model, like PRIME, was useful in building 3D structural complexes, it can't be used genome-wide, due to lacking RNA 3D structures. To take full advantage of RNA secondary structures revealed from high-throughput sequencing, we present PRIME-3D2D to predict binding sites of protein-RNA interaction. PRIME-3D ...[more]

PMID: 32678300

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