Analysis of conserved hydrophobic cores in proteins and supramolecular complexes

J Bioinform Comput Biol. 2006 Apr;4(2):357-72. doi: 10.1142/s0219720006001837.

Abstract

The conserved hydrophobic core is an important feature of a family of protein domains. We suggest a procedure for finding and the analysis of conserved hydrophobic cores. The procedure is based on using an original program called CluD (http://monkey.belozersky.msu.ru/CluD/cgi-bin/hftri.pl). Conserved hydrophobic cores of several families including homeodomains and interlock-containing domains are described. Hydrophobic clusters on some protein-DNA and protein-protein interfaces were also analyzed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Cluster Analysis
  • Conserved Sequence
  • DNA / chemistry*
  • DNA-Binding Proteins / chemistry*
  • Homeodomain Proteins / chemistry*
  • Hydrophobic and Hydrophilic Interactions
  • Macromolecular Substances / chemistry
  • Models, Chemical*
  • Models, Molecular*
  • Pattern Recognition, Automated / methods
  • Protein Binding
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • Sequence Homology, Amino Acid

Substances

  • DNA-Binding Proteins
  • Homeodomain Proteins
  • Macromolecular Substances
  • DNA