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Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and RNA Binding Sites in Rev Proteins of HIV-1 and EIAV Agree with Experimental Data
Pacific Symposium on Biocomputing
  • Michael Terribilini, Iowa State University
  • Jae-Hyung Lee, Iowa State University
  • Changhui Yan, Iowa State University
  • Robert L. Jernigan, Iowa State University
  • Susan Carpenter, Washington State University
  • Vasant Honavar, Iowa State University
  • Drena Dobbs, Iowa State University
Document Type
Conference Proceeding
Pacific Symposium on Biocomputing
Publication Version
Published Version
Publication Date
Conference Title
Pacific Symposium on Biocomputing 2006
Conference Date
January 3-7, 2006
(20.7983626, -156.33192529999997)
Protein-protein and protein nucleic acid interactions are vitally important for a wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses. We have developed machine learning approaches for predicting which amino acids of a protein participate in its interactions with other proteins and/or nucleic acids, using only the protein sequence as input. In this paper, we describe an application of classifiers trained on datasets of well-characterized protein-protein and protein-RNA complexes for which experimental structures are available. We apply these classifiers to the problem of predicting protein and RNA binding sites in the sequence of a clinically important protein for which the structure is not known: the regulatory protein Rev, essential for the replication of HIV-1 and other lentiviruses. We compare our predictions with published biochemical, genetic and partial structural information for HIV-1 and EIAV Rev and with our own published experimental mapping of RNA binding sites in EIAV Rev. The predicted and experimentally determined binding sites are in very good agreement. The ability to predict reliably the residues of a protein that directly contribute to specific binding events - without the requirement for structural information regarding either the protein or complexes in which it participates - can potentially generate new disease intervention strategies.

This is a proceeding from Pacific Symposium on Biocomputing 11 (2006): 415. Posted with permission.

PSB proceedings are published as Open Access chapters by World Scientific Publishing Company and distributed under the terms of the Creative Commons Attribution (CC BY) 4.0 License.
Copyright Owner
World Scientific
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Citation Information
Michael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, et al.. "Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and RNA Binding Sites in Rev Proteins of HIV-1 and EIAV Agree with Experimental Data" Maui, HawaiiPacific Symposium on Biocomputing Vol. 11 (2006) p. 415 - 426
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