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© Structural Dynamics Of Macromolecules
The structure of a bacterial analog of the nicotinic receptor (one color per subunit) inserted into the cell membrane (grey and orange). A representation of the volume accessible to ions is shown in yellow.
Publication : Nat. Struct. Biol.

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

Team: Architecture and Dynamics of Biological Macromolecules
Member: Marc Delarue
Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Nat. Struct. Biol. - 01 Feb 1995

Koehl P, Delarue M.

Link to Pubmed [PMID] – 7538429

Link to DOI – 10.1038/nsb0295-163

Nat Struct Biol. 1995 Feb;2(2):163-70.

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,o) 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.