Author: Rahaman, Jordon; Siltberg-Liberles, Jessica
Title: Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses Document date: 2016_11_9
ID: pygykil7_13
Snippet: A similar methodology was employed to analyze secondary structure predicted by PSIPRED (McGuffin et al. 2000) and JPred (Drozdetskiy et al. 2015) . For both predictors, the uniref90 database was used and sites were classified as loops, alpha helices, or beta strands and mapped back onto their corresponding sites in the multiple sequence alignment. This resulted in two three-state matrices for each protein family alignment, one for each predictor,.....
Document: A similar methodology was employed to analyze secondary structure predicted by PSIPRED (McGuffin et al. 2000) and JPred (Drozdetskiy et al. 2015) . For both predictors, the uniref90 database was used and sites were classified as loops, alpha helices, or beta strands and mapped back onto their corresponding sites in the multiple sequence alignment. This resulted in two three-state matrices for each protein family alignment, one for each predictor, and two binary matrices displaying secondary structure elements (alpha helix and beta strand) or loops. An additional matrix was generated to indicate sites where the secondary structure assignments differ between PSIPRED and JPred.
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