Strategies and computational tools for improving randomized protein libraries

Biomol Eng. 2005 Oct;22(4):105-12. doi: 10.1016/j.bioeng.2005.06.001.

Abstract

In the last decade, directed evolution has become a routine approach for engineering proteins with novel or altered properties. Concurrently, a trend away from purely 'blind' randomization strategies and towards more 'semi-rational' approaches has also become apparent. In this review, we discuss ways in which structural information and predictive computational tools are playing an increasingly important role in guiding the design of randomized libraries: web servers such as ConSurf-HSSP and SCHEMA allow the prediction of sites to target for producing functional variants, while algorithms such as GLUE, PEDEL and DRIVeR are useful for estimating library completeness and diversity. In addition, we review recent methodological developments that facilitate the construction of unbiased libraries, which are inherently more diverse than biased libraries and therefore more likely to yield improved variants.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.
  • Review

MeSH terms

  • Algorithms
  • Animals
  • Bacterial Proteins / chemistry
  • Computational Biology / methods
  • Directed Molecular Evolution
  • Fungal Proteins / chemistry
  • Gene Library
  • Genetic Variation
  • Humans
  • Internet
  • Models, Molecular
  • Molecular Conformation
  • Mutagenesis
  • Mutation
  • Oligonucleotides / chemistry
  • Polymerase Chain Reaction
  • Protein Engineering / methods*
  • Protein Kinase Inhibitors / chemistry
  • Proteins / chemistry*
  • Proteomics / methods
  • Recombination, Genetic
  • Software

Substances

  • Bacterial Proteins
  • Fungal Proteins
  • Oligonucleotides
  • Protein Kinase Inhibitors
  • Proteins