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Folding simulation of protein models on the structure-based cubo-octahedral lattice with the Contact Interactions algorithm

Published online by Cambridge University Press:  01 January 1999

LUCIO TOMA
Affiliation:
Dipartimento di Chimica Organica, Università di Pavia, Via Taramelli 10, 27100 Pavia, Italy
SALVATORE TOMA
Affiliation:
Pharmacia & Upjohn, Via per Pogliano, 20014 Nerviano (MI), Italy
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Abstract

Computer simulations of protein models on lattices have been widely used as an aid in the study of protein folding process. Following the suggestion of Raghunathan and Jernigan (1997, Protein Sci 6:2072–2083) that the cubo-octahedral lattice can allow a more realistic representation of proteins than other lattices, we propose here the use of a new set of internal coordinates θ for the description of a protein model on this lattice. An easy procedure for the conversion of the θ coordinates to the Cartesian coordinates is also described. When the Contact Interaction approach, already proposed by us for simulations on square or cubic lattices, was applied to the cubo-octahedral lattice, the system obeyed the correct thermodynamics derived from the definition of energy. Thus, lattice simulations of protein models, in which secondary structure elements such as α-helices or β-strands can be easily identifiable, can be performed.

Type
Research Article
Copyright
© 1999 The Protein Society

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