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Methods for Sequence–Structure Alignment

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Homology Modeling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 857))

Abstract

Homology modeling is based on the observation that related protein sequences adopt similar three-dimensional structures. Hence, a homology model of a protein can be derived using related protein structure(s) as modeling template(s). A key step in this approach is the establishment of correspondence between residues of the protein to be modeled and those of modeling template(s). This step, often referred to as sequence–structure alignment, is one of the major determinants of the accuracy of a homology model. This chapter gives an overview of methods for deriving sequence–structure alignments and discusses recent methodological developments leading to improved performance. However, no method is perfect. How to find alignment regions that may have errors and how to make improvements? This is another focus of this chapter. Finally, the chapter provides a practical guidance of how to get the most of the available tools in maximizing the accuracy of sequence–structure alignments.

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Acknowledgments

Ana Vencloviené and members of Venclovas’ lab are gratefully acknowledged for useful comments and suggestions.

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Authors and Affiliations

  1. Institute of Biotechnology, Vilnius University, Vilnius, Lithuania

    Česlovas Venclovas

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  1. Česlovas Venclovas
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Correspondence to Česlovas Venclovas .

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Editors and Affiliations

  1. Molsoft L.L.C., Sorrento Valley Road 11199, S209 San Diego, 92121, California, USA

    Andrew J. W. Orry

  2. Skaggs School of Pharmacy &, Pharmaceutical Sciences, University of California, San Diego, Gilman Drive 9500, La Jolla, 92093, California, USA

    Ruben Abagyan

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Venclovas, Č. (2011). Methods for Sequence–Structure Alignment. In: Orry, A., Abagyan, R. (eds) Homology Modeling. Methods in Molecular Biology, vol 857. Humana Press. https://doi.org/10.1007/978-1-61779-588-6_3

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  • DOI: https://doi.org/10.1007/978-1-61779-588-6_3

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