Protein structure prediction by global optimization of a potential energy function
نویسندگان
چکیده
منابع مشابه
Recent improvements in prediction of protein structure by global optimization of a potential energy function.
Recent improvements of a hierarchical ab initio or de novo approach for predicting both alpha and beta structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the ...
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An approach based exclusively on finding the global minimum of an appropriate potential energy function has been used to predict the unknown structures of five globular proteins with sizes ranging from 89 to 140 amino acid residues. Comparison of the computed lowest-energy structures of two of them (HDEA and MarA) with the crystal structures, released by the Protein Data Bank after the predicti...
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A novel hierarchical approach to protein folding has been applied to compute the unknown structures of seven target proteins provided by CASP3. The approach is based exclusively on the global optimization of a potential energy function for a united-residue model by conformational space annealing, followed by energy refinement using an all-atom potential. Comparison of the submitted models for f...
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The CGU (convex global underestimator) global optimization method is used to predict the minimum energy structures, i.e. folded states, of small protein sequences. Computational results obtained from the CGU method applied to actual protein sequences using a detailed polypeptide model and a differentiable form of the Sun/Thomas/Dill potential energy function are presented. This potential functi...
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Different components of the theoretical protein folding problem are evaluated critically. It is argued that: (i) as a rule, small- and medium-sized proteins are in the free energy minimum; (ii) long-living metastable states may either appear occasionally with growing protein size, or be selected by evolution for a specific function; (iii) functions discriminating against incorrect folds would f...
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ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 1999
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.96.10.5482