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Contact-Assisted Threading in Low-Homology Protein Modeling

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Homology Modeling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2627))

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Abstract

The ability to successfully predict the three-dimensional structure of a protein from its amino acid sequence has made considerable progress in the recent past. The progress is propelled by the improved accuracy of deep learning-based inter-residue contact map predictors coupled with the rising growth of protein sequence databases. Contact map encodes interatomic interaction information that can be exploited for highly accurate prediction of protein structures via contact map threading even for the query proteins that are not amenable to direct homology modeling. As such, contact-assisted threading has garnered considerable research effort. In this chapter, we provide an overview of existing contact-assisted threading methods while highlighting the recent advances and discussing some of the current limitations and future prospects in the application of contact-assisted threading for improving the accuracy of low-homology protein modeling.

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Acknowledgments

This work was supported in part by the National Science Foundation (IIS2030722, DBI1942692 to DB) and the National Institute of General Medical Sciences (R35GM138146 to DB).

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Authors and Affiliations

  1. Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA

    Sutanu Bhattacharya

  2. Department of Computer Science, Virginia Tech, Blacksburg, VA, USA

    Rahmatullah Roche, Md Hossain Shuvo, Bernard Moussad & Debswapna Bhattacharya

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  1. Sutanu Bhattacharya
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  2. Rahmatullah Roche
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  3. Md Hossain Shuvo
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  4. Bernard Moussad
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  5. Debswapna Bhattacharya
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Correspondence to Debswapna Bhattacharya .

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  1. Faculty of Chemistry, University of Warsaw, Warsaw, Poland

    Sławomir Filipek

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Bhattacharya, S., Roche, R., Shuvo, M.H., Moussad, B., Bhattacharya, D. (2023). Contact-Assisted Threading in Low-Homology Protein Modeling. In: Filipek, S. (eds) Homology Modeling. Methods in Molecular Biology, vol 2627. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2974-1_3

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  • DOI: https://doi.org/10.1007/978-1-0716-2974-1_3

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