Protein aggregation and amyloid fibril formation prediction software from primary sequence: towards controlling the formation of bacterial inclusion bodies

FEBS J. 2011 Jul;278(14):2428-35. doi: 10.1111/j.1742-4658.2011.08164.x. Epub 2011 May 31.


Proteins might aggregate into ordered or amorphous structures, utilizing relatively short sequence stretches, usually organized in β-sheet-like assemblies. Here, we attempt to list all available software, developed during the last decade or so, for the prediction of such aggregation-prone stretches from protein primary structure, without distinguishing whether these algorithms predict amino acid sequences destined to be involved in ordered fibrillar amyloids or amorphous aggregates. The results of application of four of these programs on 23 proteins related to amyloidoses are compared. Because protein aggregation during protein production in bacterial cell factories has been shown to resemble amyloid formation, the algorithms might become useful tools to improve the solubility of recombinant proteins and for screening therapeutic approaches against amyloidoses under conditions that mimic physiologically relevant environments. One such example is given.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Amyloid / biosynthesis
  • Amyloid / chemistry*
  • Animals
  • Gram-Negative Bacteria / metabolism
  • Gram-Positive Bacteria / metabolism
  • Humans
  • Inclusion Bodies / metabolism*
  • Industrial Microbiology / methods*
  • Internet
  • Protein Folding*
  • Recombinant Proteins / biosynthesis
  • Recombinant Proteins / chemistry*
  • Software*
  • Solubility


  • Amyloid
  • Recombinant Proteins