An immune algorithm for protein structure prediction on lattice models

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An immune algorithm for protein structure prediction on lattice models (2004)

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by Vincenzo Cutello , Mario Pavone , Jonathan Timmis

Venue:	IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION
Citations:	43 - 10 self

BibTeX

@ARTICLE{Cutello04animmune,
    author = {Vincenzo Cutello and Mario Pavone and Jonathan Timmis},
    title = {An immune algorithm for protein structure prediction on lattice models},
    journal = {IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION},
    year = {2004},
    pages = {101--117}
}

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Abstract

We present an Immune Algorithm (IA) inspired by the clonal selection principle, which has been designed for the protein structure prediction problem (PSP). The proposed IA employs two special mutation operators, hypermutation and hypermacromutation, to allow for effective searching, and an aging mechanism, a new immune inspired operator, devised to enforce diversity in the population during evolution. When cast as an optimization problem, the PSP can be seen as discovering a protein conformation with minimal energy. The proposed IA was tested on well known PSP lattice models, the HP model in 2D and 3D square lattices’, and the functional model protein, which is a more realistic biological model. Our experimental results demonstrate that the proposed Immune Algorithm is very competitive with existing state-of-art algorithms for the PSP on lattice models. Index Terms — Immune algorithms, clonal selection algorithms, hypermutation operator, hypermacromutation operator, aging operator, protein structure prediction problem, 2D HP model, 3D HP model, functional model proteins.

Keyphrases

immune algorithm lattice model hp model protein structure prediction protein structure prediction problem functional model protein square lattice realistic biological model psp lattice model protein conformation minimal energy clonal selection algorithm clonal selection principle effective searching new immune optimization problem state-of-art algorithm hypermacromutation operator hypermutation operator special mutation operator index term immune algorithm experimental result

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