Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity.

Lianyi Han, Juan Cui, Honghuang Lin, Zhiliang Ji, Zhiwei Cao, Yixue Li, Yuzong Chen

Research output: Contribution to journalReview articlepeer-review

61 Scopus citations

Abstract

Protein sequence contains clues to its function. Functional prediction from sequence presents a challenge particularly for proteins that have low or no sequence similarity to proteins of known function. Recently, machine learning methods have been explored for predicting functional class of proteins from sequence-derived properties independent of sequence similarity, which showed promising potential for low- and non-homologous proteins. These methods can thus be explored as potential tools to complement alignment- and clustering-based methods for predicting protein function. This article reviews the strategies, current progresses, and underlying difficulties in using machine learning methods for predicting the functional class of proteins. The relevant software and web-servers are described. The reported prediction performances in the application of these methods are also presented, which need to be interpreted with caution as they are dependent on such factors as datasets used and choice of parameters.

Original languageEnglish (US)
Pages (from-to)4023-4037
Number of pages15
JournalProteomics
Volume6
Issue number14
DOIs
StatePublished - Jul 2006
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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