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Folding simulation of protein models on the structure‐based cubo‐octahedral lattice with the Contact Interactions algorithm
Author(s) -
Toma Lucio,
Toma Salvatore
Publication year - 1999
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.8.1.196
Subject(s) - protein folding , lattice protein , computer science , lattice (music) , algorithm , folding (dsp implementation) , octahedron , crystallography , chemistry , crystal structure , physics , engineering , acoustics , biochemistry , electrical engineering
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 cubooctahedral 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.