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A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling

Nature Structural Biology volume 2, pages 163–170 (1995)Cite this article

Abstract

A new computational procedure which simultaneously provides gap closure and side-chain positioning in homology modelling is described. It uses a database search scheme to generate fragments to model gaps, a rotamer library to define side-chain conformations, and iteratively refines a conformational matrix CM, such that its elements CM(i,j,0) and CM(i,j,k) give the probabilities that the backbone of residue i adopts the conformation described by fragment j and that its side-chain adopts the conformation of its possible rotamer k. Each residue experiences the average of all possible environments, weighted by their respective probabilities. The method converges, thereby deserving the name of ‘self consistent mean field’ approach.

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Authors and Affiliations

  1. UPR 9003 du C.N.R.S., ESBS, Boulevard Sébastien Brant, 67400, Illkirch Graffenstaden, France

    Patrice Koehl

  2. Laboratoire d'lmmunologie Structurale, Institut Pasteur, 25 rue du Docteur Roux, 75015, Paris, France

    Marc Delarue

  3. UPR 9002 du C.N.R.S., I.B.M.C, 15 rue René Descartes, 67084, Strasbourg Cedex, France

    Marc Delarue

Authors
  1. Patrice Koehl
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  2. Marc Delarue
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Koehl, P., Delarue, M. A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling. Nat Struct Mol Biol 2, 163–170 (1995). https://doi.org/10.1038/nsb0295-163

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