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Table 2 Precision for detecting contact versus non-contact residues at 20% recall, for sub-alignments of 70%

From: Mutual information and variants for protein domain-domain contact prediction

Contact prediction for sub-alignments
MI variant 70% AVG 70% STD DEV 100%
MIc 52.5* 2.1 54.8
MIp 46.0* 2.1 47.4
MIcRA 41.9* 1.8 41.4
MIpRA 38.2* 1.5 38.5
MIp3D 30.6 1.3 28.5
MIRA 30.2* 1.2 31.4
MIp3DRA 28.0* 1.2 30.9
MI 25.8* 0.8 27.6
MI3DRA 23.2* 1.0 25.5
Random - - 24.4
RandomRA - - 24.4
MI3D 20.0 0.6 21.8
  1. 70% of sequences in an MSA were randomly selected and the 10 MI variant scores based on the new sub-alignment were calculated. This subset selection and calculation procedure was repeated 100 times for those test cases that had ≥200 sequences to ensure ≥125 sequences in each sub-alignment[8]. Thus 24 test cases were used. For each of the 100 iterations a P-ROC curve similar to Figure2 was plotted for the 24 test cases (figures not shown), and the precision at 20% recall recorded. Columns one and two, respectively, contain the averages and standard deviations of these 100 precision values. Column three indicates the precision attained at 20% recall when all sequences in the 24 original MSAs were used. When considering this set of 24 cases, the probability of randomly selecting a contact residue from all surface residues is 24.4% generally and when using the reduced alphabet MSAs. The MI variants are listed in descending order of the average precision of the 100 70% sub- alignments. The presence of an ‘*’ at an MI variant indicates that the difference between the precision of this MI variant and the next lowest is significant at the 0.1% level, when using two-sample t-tests with a sample size of 24.
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