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All the operators were kept at default settings.
The pipeline parameters were kept at default settings.
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All BLAST searches were done without the low-complexity filter and with all other settings kept at default.
Atom types for both protein and ligand were generated automatically and all ligand flexibility terms were turned on, although Ring-NH2 and Ring-NR1R2 were set to flip, other settings were kept at default.
The other docking parameters were kept at default values.
The cost parameter was kept at default as 1 and class weights were kept even.
One parameter is varied at a time, while the other two are kept at default values.
Prior probabilities were kept at their default settings for standard (morphological) analyses.
All other settings in MSATCOMMANDER were kept at defaults.
High-quality reads were selected using Newbler sequence filtering at default settings.
Secondary structure predictions of aptamers were calculated using the NUPACK web application46 (http://www.nupack.org/) at default settings at 37 °C.
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