Biomathematical description of synthetic peptide libraries

PLoS One. 2015 Jun 4;10(6):e0129200. doi: 10.1371/journal.pone.0129200. eCollection 2015.

Abstract

Libraries of randomised peptides displayed on phages or viral particles are essential tools in a wide spectrum of applications. However, there is only limited understanding of a library's fundamental dynamics and the influences of encoding schemes and sizes on their quality. Numeric properties of libraries, such as the expected number of different peptides and the library's coverage, have long been in use as measures of a library's quality. Here, we present a graphical framework of these measures together with a library's relative efficiency to help to describe libraries in enough detail for researchers to plan new experiments in a more informed manner. In particular, these values allow us to answer-in a probabilistic fashion-the question of whether a specific library does indeed contain one of the "best" possible peptides. The framework is implemented in a web-interface based on two packages, discreteRV and peptider, to the statistical software environment R. We further provide a user-friendly web-interface called PeLiCa (Peptide Library Calculator, http://www.pelica.org), allowing scientists to plan and analyse their peptide libraries.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Molecular Sequence Data
  • Peptide Library*
  • Peptides / chemistry
  • Probability
  • Software*

Substances

  • Peptide Library
  • Peptides

Grants and funding

This work was supported by Deutsche Krebshilfe (http://www.krebshilfe.de/metanavigation/english.html, grant 110902 to MT). MT was also supported by the Margarethe Clemens Foundation (http://themargaretclemonsfoundation.org/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.