LINUS: A hierarchic procedure to predict the fold of a protein

Rajgopal Srinivasan, George D. Rose

Research output: Contribution to journalArticle

Abstract

We describe LINUS, a hierarchic procedure to predict the fold of a protein from its amino acid sequence alone. The algorithm, which has been implemented in a computer program, was applied to large, overlapping fragments from a diverse test set of 7 X‐ray‐elucidated proteins, with encouraging results. For all proteins but one, the overall fragment topology is well predicted, including both secondary and supersecondary structure. The algorithm was also applied to a molecule of unknown conformation, groES, inwhich X‐ray structure determination is presently ongoing. LINUS is an acronym for Local Independently Nucleated Units of Structure. The procedure ascends the folding hierarchy in discrete stages, with concomitant accretion of structure at each step. The chain is represented by simplified geometry and folds under the influence of a primitive energy function. The only accurately described energetic quantity in this work is hard sphere repulsion–the principal forceinvolved in organizing protein conformation [Richards, F. M. Ann. Rev. Biophys. Bioeng. 6:151–176, 1977]. Among other applications, the method is a natural tool for use in the human genome initiative. © 1995 Wiley‐Liss, Inc.

Original languageEnglish (US)
Pages (from-to)81-99
Number of pages19
JournalProteins: Structure, Function, and Bioinformatics
Volume22
Issue number2
DOIs
StatePublished - Jun 1995

Keywords

  • protein folding

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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