Improving protein-RNA interface prediction by combining sequence homology based method with a naive bayes classifier: Preliminary results

Li C. Xue, Rasna Walia, Yasser EL-Manzalawy, Drena Dobbs, Vasant Honavar

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Protein-RNA interactions play important roles in cellular processes like protein synthesis, RNA processing, and gene expression regulation. Reliable identification of the interfaces involved in RNA-protein interactions is essential for comprehending the mechanisms and the functional implications of these interactions and provides a valuable guide for rational drug discovery and design. Because the determination of 3D structures of protein-RNA complexes has various technical limitations and is typically costly, reliable in silico interface prediction methods that require only the sequence information are urgently needed. We present HomPRIP, a homologous sequence based method for predicting protein-RNA interfaces, based on our conservation analysis of protein-RNA interfaces. We test Hom-PRIP on a benchmark dataset of 199 proteins and compare it with the state-of-the-art protein-RNA interface prediction methods. Our results show that HomPRIP can reliably identify protein-RNA interface residues in 71% of test proteins with at least one putative sequence homolog passing the similarity thresholds of HomPRIP. Moreover, to facilitate predictions for proteins with no identified homologs, we develop HomPRIP-NB, a method combining the HomPRIP predictor and a Naive Bayes (NB) classifier trained using evolutionary information derived from alignments against the NCBI nr database. Our results suggest that HomPRIP-NB significantly outperforms the state-of-the-art machine learning methods for predicting protein-RNA interface residues.

Original languageEnglish (US)
Title of host publication2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011
Pages556-558
Number of pages3
DOIs
StatePublished - Dec 1 2011
Event2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011 - Chicago, IL, United States
Duration: Aug 1 2011Aug 3 2011

Other

Other2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011
CountryUnited States
CityChicago, IL
Period8/1/118/3/11

Fingerprint

Sequence Homology
RNA
Classifiers
Proteins
Gene expression regulation
Benchmarking
Drug Design
Gene Expression Regulation
Drug Discovery
Computer Simulation
Learning systems
Conservation
Databases

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

Xue, L. C., Walia, R., EL-Manzalawy, Y., Dobbs, D., & Honavar, V. (2011). Improving protein-RNA interface prediction by combining sequence homology based method with a naive bayes classifier: Preliminary results. In 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011 (pp. 556-558) https://doi.org/10.1145/2147805.2147899
Xue, Li C. ; Walia, Rasna ; EL-Manzalawy, Yasser ; Dobbs, Drena ; Honavar, Vasant. / Improving protein-RNA interface prediction by combining sequence homology based method with a naive bayes classifier : Preliminary results. 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. 2011. pp. 556-558
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Xue, LC, Walia, R, EL-Manzalawy, Y, Dobbs, D & Honavar, V 2011, Improving protein-RNA interface prediction by combining sequence homology based method with a naive bayes classifier: Preliminary results. in 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. pp. 556-558, 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011, Chicago, IL, United States, 8/1/11. https://doi.org/10.1145/2147805.2147899

Improving protein-RNA interface prediction by combining sequence homology based method with a naive bayes classifier : Preliminary results. / Xue, Li C.; Walia, Rasna; EL-Manzalawy, Yasser; Dobbs, Drena; Honavar, Vasant.

2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. 2011. p. 556-558.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Xue LC, Walia R, EL-Manzalawy Y, Dobbs D, Honavar V. Improving protein-RNA interface prediction by combining sequence homology based method with a naive bayes classifier: Preliminary results. In 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. 2011. p. 556-558 https://doi.org/10.1145/2147805.2147899