3D modeling for TM receptors: Algorithms and validations

Gregory V. Nikiforovich, Stan Galaktionov, Vladimir M. Tseitin, David R. Lowis, Mark D. Shenderovich, Garland R. Marshall

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

This paper outlines the basic strategy to build 3D models of transmembrane G-protein coupled receptors (GPCRs) starting from their amino acid sequences in a 'block-by-block' manner: (i) locate possible TM helical fragments in the GPCR sequence; (ii) build 3D structures for these helices; (iii) arrange isolated helices across the membrane; (iv) calculate all pairwise helix-helix interactions; (v) assemble helical bundle(s); (vi) restore interhelical loops and N- and C-termini; and (vii) refine the entire 3D structure(s). Computer algorithms and preliminary results for most of the steps are discussed.

Original languageEnglish
Pages (from-to)413-415
Number of pages3
JournalLetters in Peptide Science
Volume5
Issue number5-6
DOIs
StatePublished - Jan 1 1998

Keywords

  • Energy calculations
  • Molecular modeling
  • Transmembrane receptors

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