Comparison of different methods for the prediction of critical residues in protein interfaces using a BID derived dataset as described in Tuncbag et al. [18].
Joan Segura Mora
Salam A. Assi
Narcis Fernandez-Fuentes
10.1371/journal.pone.0012352.t001
https://plos.figshare.com/articles/dataset/_Comparison_of_different_methods_for_the_prediction_of_critical_residues_in_protein_interfaces_using_a_BID_derived_dataset_as_described_in_Tuncbag_et_al_18_/504770
a<p>Predictions were performed using PCRPi <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012352#pone.0012352-Assi1" target="_blank">[7]</a> with an expert BN trained in a Ab+ dataset that does not include the crystal structure of the c2 fragment of streptococcal protein G in complex with the Fc domain of human Ig (PDB code 1fcc).</p>b<p>Values were obtained running FoldX <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012352#pone.0012352-Guerois1" target="_blank">[19]</a> with default parameters and a ddG<sub>binding</sub> cut-off of 2.0 Kcal.mol<sup>−1</sup> (i.e. residues were considered critical if upon mutation to Ala, predicted ddG<sub>binding</sub>≥2.0 Kcal.mol<sup>−1</sup>).</p>c<p>Precision, recall, and F1 score values taken from Tuncbag et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012352#pone.0012352-Tuncbag1" target="_blank">[18]</a>.</p>
2013-02-20 23:51:23
methods
residues
interfaces
derived
dataset
tuncbag
et