LearnCoil-VMF: Computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins

Mona Singh, Bonnie Berger, Peter S. Kim

Research output: Contribution to journalArticlepeer-review

137 Scopus citations


Crystallographic studies have shown that the coiled-coil motif occurs in several viral membrane-fusion proteins, including HIV-1 gp41 and influenza virus hemagglutinin. Here, the LearnCoil-VMF program was designed as a specialized program for identifying coiled-coil-like regions in viral membrane-fusion proteins. Based upon the use of LearnCoil-VMF, as well as other computational tools, we report detailed sequence analyses of coiled-coil-like regions in retrovirus, paramyxovirus and filo-virus membrane-fusion proteins. Additionally, sequence analyses of these proteins outside their putative coiled-coil domains illustrate some structural differences between them. Complementing previous crystallographic studies, the coiled-coil-like regions detected by LearnCoil-VMF provide further evidence that the three-stranded coiled coil is a common motif found in many diverse viral membrane-fusion proteins. The abundance and structural conservation of this motif, even in the absence of sequence homology, suggests that it is critical for viral-cellular membrane fusion. The LearnCoil-VMF program is available at http://web.wi.mit.edu/kim.

Original languageEnglish (US)
Pages (from-to)1031-1041
Number of pages11
JournalJournal of Molecular Biology
Issue number5
StatePublished - Jul 30 1999
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Structural Biology


  • Coiled coil
  • Computational methods
  • Filovirus
  • Paramyxovirus
  • Retrovirus
  • Viral membrane fusion


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