Critical assessment of side chain conformation prediction in modelling of single point amino acid mutation

Anna Marabotti, Angelo Facchiano

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

We assessed the ability of three widely used and freely available programs for side chain repacking to simulate the structural effects of single point mutations. The programs tested seem to produce sufficiently reliable predictions only when mutations involve residues characterized by limited flexibility. The change in size and/or polarity of the mutant side chain can affect the performances of the different programs. The correlation between the quality of predictions, exposure to solvent, and B-factors of the corresponding residues in crystal is also investigated. This analysis may provide non-experts with insights into what types of modelling protocols work best for such a problem as well as providing information to developers for improving their algorithms.

Original languageEnglish
Title of host publicationAdvances in Experimental Medicine and Biology
Pages283-289
Number of pages7
Volume680
DOIs
Publication statusPublished - 2010

Publication series

NameAdvances in Experimental Medicine and Biology
Volume680
ISSN (Print)00652598

Fingerprint

Point Mutation
Conformations
Amino Acids
Mutation
Crystals
3'-(1-butylphosphoryl)adenosine

Keywords

  • Amino acid
  • Conformation prediction
  • Mutation
  • Protein structure
  • Quality of predictions

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Marabotti, A., & Facchiano, A. (2010). Critical assessment of side chain conformation prediction in modelling of single point amino acid mutation. In Advances in Experimental Medicine and Biology (Vol. 680, pp. 283-289). (Advances in Experimental Medicine and Biology; Vol. 680). https://doi.org/10.1007/978-1-4419-5913-3_32

Critical assessment of side chain conformation prediction in modelling of single point amino acid mutation. / Marabotti, Anna; Facchiano, Angelo.

Advances in Experimental Medicine and Biology. Vol. 680 2010. p. 283-289 (Advances in Experimental Medicine and Biology; Vol. 680).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Marabotti, A & Facchiano, A 2010, Critical assessment of side chain conformation prediction in modelling of single point amino acid mutation. in Advances in Experimental Medicine and Biology. vol. 680, Advances in Experimental Medicine and Biology, vol. 680, pp. 283-289. https://doi.org/10.1007/978-1-4419-5913-3_32
Marabotti A, Facchiano A. Critical assessment of side chain conformation prediction in modelling of single point amino acid mutation. In Advances in Experimental Medicine and Biology. Vol. 680. 2010. p. 283-289. (Advances in Experimental Medicine and Biology). https://doi.org/10.1007/978-1-4419-5913-3_32
Marabotti, Anna ; Facchiano, Angelo. / Critical assessment of side chain conformation prediction in modelling of single point amino acid mutation. Advances in Experimental Medicine and Biology. Vol. 680 2010. pp. 283-289 (Advances in Experimental Medicine and Biology).
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