title: MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers.
abstract: Aptamers are 'synthetic antibodies' that can bind to target molecules with high affinity and specificity. Aptamers are chemically synthesized and their discovery can be performed completely in vitro, rather than relying on in vivo biological processes, making them well-suited for high-throughput discovery. However, a large fraction of the most enriched aptamers in Systematic Evolution of Ligands by EXponential enrichment (SELEX) rounds display poor binding activity. Here, we present MPBind, a Meta-motif-based statistical framework and pipeline to Predict the BIND: ing potential of SELEX-derived aptamers. Using human embryonic stem cell SELEX-Seq data, MPBind achieved high prediction accuracy for binding potential. Further analysis showed that MPBind is robust to both polymerase chain reaction amplification bias and incomplete sequencing of aptamer pools. These two biases usually confound aptamer analysis.
  
  
  METHODS
  MPBind software and documents are available at http://www.morgridge.net/MPBind.html. The human embryonic stem cells whole-cell SELEX-Seq data are available at http://www.morgridge.net/Aptamer/.
authors.affiliation: Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Peng
authors.initials: P
authors.lastname: Jiang
authors.affiliation: Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Susanne
authors.initials: S
authors.lastname: Meyer
authors.affiliation: Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Zhonggang
authors.initials: Z
authors.lastname: Hou
authors.affiliation: Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Propson
authors.affiliation: Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: H Tom
authors.initials: HT
authors.lastname: Soh
authors.affiliation: Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: James A
authors.initials: JA
authors.lastname: Thomson
authors.affiliation: Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, Departments of Mechanical Engineering and Materials, University of California, Santa Barbara, CA 93106 and Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Ron
authors.initials: R
authors.lastname: Stewart
mesh_terms: D052157:Aptamers, Nucleotide / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D053595:Embryonic Stem Cells / Q000378:metabolism; D006801:Humans; D008024:Ligands; D009841:Oligonucleotides / Q000378:metabolism; D052156:SELEX Aptamer Technique; D017421:Sequence Analysis; D012984:Software; D013379:Substrate Specificity
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D009841:Oligonucleotides