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Performance comparison of computational methods for modeling alpha-helical structures

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Abstract

Geometry optimization results are reported for secondary structural elements of small proteins and polypeptides. Emphasis is placed on how well molecular mechanics as well as semiempirical, ab initio, and density functional methods describe α-helical and related structures in purely theoretical models (Gly10, Ile10) as well as in realistic models (an α-helical region of calmodulin, and the complete structure of a small protein). Many of the methods examined here were found to provide unsatisfactory descriptions of the hydrogen-bonding interactions within polypeptide-type structures, as the α-helical canonical secondary structure motif was not reproduced accurately. Ab initio and DFT methods provided reasonable results only when solvation models were included, although Hartree–Fock failed even with solvation in one of the test cases; among the semiempirical methods, one of the PM6 implementations performed very well.

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Acknowledgments

Funding from the Romanian Ministry of Education and Research (grants PN II 312/2008 and Parteneriate 72168/2008-FLUORODENT) is gratefully acknowledged.

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Authors and Affiliations

  1. Department of Chemistry and Chemical Engineering, Babes-Bolyai University, 11 Arany Janos str, Cluj-Napoca, 400028, Romania

    Alexandru Lupan, Attila-Zsolt Kun, Francisco Carrascoza & Radu Silaghi-Dumitrescu

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  1. Alexandru Lupan
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  2. Attila-Zsolt Kun
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  3. Francisco Carrascoza
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  4. Radu Silaghi-Dumitrescu
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Correspondence to Radu Silaghi-Dumitrescu.

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Lupan, A., Kun, AZ., Carrascoza, F. et al. Performance comparison of computational methods for modeling alpha-helical structures. J Mol Model 19, 193–203 (2013). https://doi.org/10.1007/s00894-012-1531-z

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