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Mitra R, Cohen AS, Tang WY, Hosseini H, Hong Y, Berman HM, Rohs R. RNAproDB: A Webserver and Interactive Database for Analyzing Protein-RNA Interactions. J Mol Biol 2025:169012. [PMID: 40126909 DOI: 10.1016/j.jmb.2025.169012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2024] [Revised: 02/09/2025] [Accepted: 02/12/2025] [Indexed: 03/26/2025]
Abstract
We present RNAproDB (https://rnaprodb.usc.edu/), a new webserver, analysis pipeline, database, and highly interactive visualization tool, designed for protein-RNA complexes, and applicable to all forms of nucleic acid containing structures. RNAproDB computes several mapping schemes to place nucleic acid components and present protein-RNA interactions appropriately. Various structural annotations are computed including non-canonical base-pairing geometries, hydrogen bonds, and protein-RNA and RNA-RNA water-mediated interactions. This information is presented through integrated visualization and data tools. Subgraph selection facilitates studying smaller components of the interface. Molecular surface electrostatic potential can be visualized. RNAproDB enables analyzing and exploring experimentally determined, predicted, and designed protein-nucleic acid complexes. We present a quantitative analysis of pre-analyzed protein-RNA structures in RNAproDB revealing statistical patterns of molecular binding and recognition.
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Affiliation(s)
- Raktim Mitra
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Ari S Cohen
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Wei Yu Tang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Hirad Hosseini
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Yongchan Hong
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Helen M Berman
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Department of Physics & Astronomy, University of Southern California, Los Angeles, CA 90089, USA; Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA; Department of Medicine, Division of Medical Oncology, University of Southern California, Los Angeles, CA 90033, USA.
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