Predicting protein folding cores by empirical potential functions
نویسندگان
چکیده
منابع مشابه
Protein folding potential functions
There has been a great deal of activity recently on approaches to the calculation of protein folding using specially devised empirical potential functions. We have developed one such function that solves the protein structure recognition problem: given the sequence for a globular protein and a collection of plausible protein conformations, including the native conformation for that sequence, id...
متن کاملLearning about protein folding via potential functions.
Over the last few years we have developed an empirical potential function that solves the protein structure recognition problem: given the sequence for an n-residue globular protein and a collection of plausible protein conformations, including the native conformation for that sequence, identify the correct, native conformation. Having determined this potential on the basis of only some 6500 na...
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Simplified models and empirical potentials are being increasingly used for the analysis of proteins, frequently augmenting or replacing molecular mechanics approaches. Recent folding simulations have employed potentials that, in addition to terms assuring proper polypeptide geometry, include only two noncovalent effects-hydrogen bonding and hydrophobicity, with extremely simple approximations t...
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A structured folding pathway, which is a time ordered sequence of folding events, plays an important role in the protein folding process and hence, in the conformational search. Pathway prediction, thus gives more insight into the folding process and is a valuable guiding tool to search the conformation space. In this paper, we propose a novel 'unfolding' approach to predict the folding pathway...
متن کاملHow optimization of potential functions affects protein folding.
The relationship between the optimization of the potential function and the foldability of theoretical protein models is studied based on investigations of a 27-mer cubic-lattice protein model and a more realistic lattice model for the protein crambin. In both the simple and the more complicated systems, optimization of the energy parameters achieves significant improvements in the statistical-...
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ژورنال
عنوان ژورنال: Archives of Biochemistry and Biophysics
سال: 2009
ISSN: 0003-9861
DOI: 10.1016/j.abb.2008.12.011