PMID: 9194160Apr 1, 1997Paper

Prediction of protein side chain conformations: a study on the influence of backbone accuracy on conformation stability in the rotamer space

Protein Engineering
P TufferyS Hazout

Abstract

We have studied the effect of backbone inaccuracy on the efficiency of protein side chain conformation prediction using rotamer libraries. The backbones were generated by randomly perturbing the crystallographic conformation of 12 proteins and exhibit C alpha r.m.s.d.s of up to 2 A. Our results show that, even for a perturbation of the backbone fully compatible with the temperature factors of the proteins, the predicted side chain conformations of approximately 10% of the buried side chains remain variable. This fraction increases further for larger backbone deviations. However, for backbone deviations of up to 2 A r.m.s.d., the predicted side chain r.m.s.d. varies only in a ratio of < 1.4. Moreover, a possible strategy for obtaining side chain conformations close to the experimental ones consists of extracting the consensus conformations of the side chains from a series of backbone conformations. Such a procedure allows the computation of the side chain conformations with no loss of accuracy for backbones exhibiting r.m.s.d.s of up to 1 A from the crystallographic coordinates. For larger backbone deviations (up to 2 A r.m.s.d.) the r.m.s.d. of the buried side chains increases from 1.33 up to 1.60 A. We also discuss the influen...Continue Reading

Citations

Jan 20, 1999·Proceedings of the National Academy of Sciences of the United States of America·S C LovellD C Richardson
Jan 10, 2003·Nucleic Acids Research·S S SheikK Sekar
Jul 5, 2002·Journal of Molecular Biology·Matthew P JacobsonBarry Honig
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Sep 25, 2004·Protein Science : a Publication of the Protein Society·Jim Warwicker
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Nov 26, 2008·Journal of Molecular Graphics & Modelling·Amaury Pupo, Ernesto Moreno
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Sep 9, 2017·Journal of Chemical Theory and Computation·Thomas Gaillard, Thomas Simonson

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