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Loop Simulations

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Homology Modeling

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

Abstract

Loop modeling is crucial for high-quality homology model construction outside conserved secondary structure elements. Dozens of loop modeling protocols involving a range of database and ab initio search algorithms and a variety of scoring functions have been proposed. Knowledge-based loop modeling methods are very fast and some can successfully and reliably predict loops up to about eight residues long. Several recent ab initio loop simulation methods can be used to construct accurate models of loops up to 12–13 residues long, albeit at a substantial computational cost. Major current challenges are the simulations of loops longer than 12–13 residues, the modeling of multiple interacting flexible loops, and the sensitivity of the loop predictions to the accuracy of the loop environment.

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  1. Molsoft L.L.C., San Diego, CA, USA

    Maxim Totrov

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  1. Maxim Totrov
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Correspondence to Maxim Totrov .

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  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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Totrov, M. (2011). Loop Simulations. 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_9

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  • DOI: https://doi.org/10.1007/978-1-61779-588-6_9

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