MPBind

MPBind is a software tool that uses a Meta-motif-based statistical framework and pipeline to predict the binding potential of aptamers derived from SELEX rounds. Aptamers are synthetic antibodies that can bind to target molecules with high affinity and specificity, and their discovery can be performed completely in vitro, making them well-suited for high-throughput discovery. However, a large fraction of the most enriched aptamers in SELEX rounds display poor binding activity. MPBind achieved high prediction accuracy for binding potential using human embryonic stem cell SELEX-Seq data. Further analysis showed that MPBind is robust to both polymerase chain reaction amplification bias and incomplete sequencing of aptamer pools, which usually confound aptamer analysis.