Critical assessment of side chain conformation prediction in modelling of single point amino acid mutation
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Updated: Jun 8, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Anna Marabotti1, Angelo Facchiano
1Institute of Biomedical Technologies, National Research Council, Via F.lli Cervi 92, 20090 Segrate, MI, Italy. anna.marabotti@itb.cnr.it
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.
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