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© IRL Press Limited

FUS: a system to simulate conformational changes in biological macromolecules

FranÇois Major , Richard Feldmann 1, Guy Lapalme and Robert Cedergren *,*

Département d'Informatique et Recherche Opérationnelle, Université de Montréal, Case postale 6128, Succursale A Montréal, Québec, Canada H3C 3J7
1Division of Computer Research and Technology, National Institutes of Health Bethesda, MD 20892, USA
*Département de Biochimie, Université de Montréal, Case postale 6128, Succursale A Montréal, Québec, Canada H3C 3J7

*To whom reprint requests should be sent

In order to study the dynamics of protein and nucleic acid conformations, a molecular folding-unfolding system (FUS written in Lisp) has been developed. Secondary structure features of protein and nucleic acids are graphically represented by cubes in a modified ‘Blocks World’ paradigm. Modeling of protein and nucleic acid unfolding (denaturation) and folding of their three-dimensional structure is possible by the use of high level ‘block’ operators which allow displacement of these structural features in space. Due to the flexible nature of this program, FUS is a useful tool for the rapid evaluation of user-defined rules governing conformational changes. The use of FUS to unfold three common proteins (prealbumin, flavodoxin and triose phosphate isomerase) and a tRNA is presented.

Received on March 22, 1988; accepted on June 1, 1988

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