HDX-Analyzer: a novel package for statistical analysis of protein structure dynamics

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Liu S., Liu L., UZUNER U., Zhou X., Gu M., Shi W., ...Daha Fazla

BMC BIOINFORMATICS, cilt.12, 2011 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 12
  • Basım Tarihi: 2011
  • Doi Numarası: 10.1186/1471-2105-12-s1-s43
  • Dergi Adı: BMC BIOINFORMATICS
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Karadeniz Teknik Üniversitesi Adresli: Hayır

Özet

Background: HDX mass spectrometry is a powerful platform to probe protein structure dynamics during ligand binding, protein folding, enzyme catalysis, and such. HDX mass spectrometry analysis derives the protein structure dynamics based on the mass increase of a protein of which the backbone protons exchanged with solvent deuterium. Coupled with enzyme digestion and MS/MS analysis, HDX mass spectrometry can be used to study the regional dynamics of protein based on the m/z value or percentage of deuterium incorporation for the digested peptides in the HDX experiments. Various software packages have been developed to analyze HDX mass spectrometry data. Despite the progresses, proper and explicit statistical treatment is still lacking in most of the current HDX mass spectrometry software. In order to address this issue, we have developed the HDXanalyzer for the statistical analysis of HDX mass spectrometry data using R, Python, and RPY2.