Construction of Protein Tertiary Structures Using a Hierarchical Approach

Construction of Protein Tertiary Structures Using a Hierarchical Approach (2000)

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by Yu Xia , Enoch S. Huang , Michael Levitt , Ram Samudrala

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J. Mol. Biol

BibTeX

@ARTICLE{Xia00constructionof,
    author = {Yu Xia and Enoch S. Huang and Michael Levitt and Ram Samudrala},
    title = {Construction of Protein Tertiary Structures Using a Hierarchical Approach},
    journal = {J. Mol. Biol},
    year = {2000},
    volume = {300},
    pages = {171--185}
}

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Abstract

Ab initio protein structure prediction remains one of the most important unsolved problems in molecular biophysics after 30 years of intensive research. This problem is in principle solvable: if we know the exact formulation of the physical micro-environment within a cell where proteins fold, we will be able to mimic the folding process in nature by computing the molecular dynamics based on our knowledge of the physical laws (McCarmmon & Harvey, 1987; van Gunsteren, 1998; Duan & Kollman, 1998). Complementarily, we can rely on the much-debated thermodynamic hypothesis, i.e. that the native protein structure is thermodynamically stable and is located at the global free energy minimum (Annsen, 1973). However, we do not yet have a complete understanding of the driving forces behind protein folding. Perturbations introduced by errors in the potential energy landscape may possibly result in a different folding pathway and a different folded structure. Even if we have an accurat...

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