In silico prediction of protein flexibility with local structure approach

Biochimie
Tarun Jairaj NarwaniAlexandre G de Brevern

Abstract

Flexibility is an intrinsic essential feature of protein structures, directly linked to their functions. To this day, most of the prediction methods use the crystallographic data (namely B-factors) as the only indicator of protein's inner flexibility and predicts them as rigid or flexible. PredyFlexy stands differently from other approaches as it relies on the definition of protein flexibility (i) not only taken from crystallographic data, but also (ii) from Root Mean Square Fluctuation (RMSFs) observed in Molecular Dynamics simulations. It also uses a specific representation of protein structures, named Long Structural Prototypes (LSPs). From Position-Specific Scoring Matrix, the 120 LSPs are predicted with a good accuracy and directly used to predict (i) the protein flexibility in three categories (flexible, intermediate and rigid), (ii) the normalized B-factors, (iii) the normalized RMSFs, and (iv) a confidence index. Prediction accuracy among these three classes is equivalent to the best two class prediction methods, while the normalized B-factors and normalized RMSFs have a good correlation with experimental and in silico values. Thus, PredyFlexy is a unique approach, which is of major utility for the scientific community....Continue Reading

References

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Citations

Jan 15, 2021·Platelets·Nora El JahraniAlexandre G de Brevern
Sep 19, 2020·Biochimie·Alexandre G de Brevern
Aug 13, 2021·Bioinformatics·Dominik SchwarzCharlotte M Deane
Nov 13, 2021·Journal of Biomolecular Structure & Dynamics·Amer M AlanaziAli Saber Abdelhameed

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