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LINUS: A hierarchic procedure to predict the fold of a protein
Author(s) -
Srinivasan Rajgopal,
Rose George D.
Publication year - 1995
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340220202
Subject(s) - fold (higher order function) , computer science , computational biology , chemistry , biology , programming language
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 L ocal I ndependently N ucleated U nits of S tructure. 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.