Protein folding, potential energy surfaces

Keywords, protein folding, tertiary structure, potential energy surface, global optimization, empirical potential, residue potential, surface potential, parameter estimation, density estimation, cluster analysis, quadratic programming... 

KD Ball, RS Beii y, RE Kunz, E-Y Li, A Proykova, DJ Wales. Erom topographies to dynamics of multidimensional potential energy surfaces of atomic clusters. Science 271 963-966, 1996. RS Berry, N Elmaci, JP Rose, B Vekhter. Linking topography of its potential surface with the dynamics of folding of a protein model. Proc Natl Acad Sci USA 94 9520-9524, 1997. Z Guo, D Thii-umalai. J Mol Biol 263 323-343, 1996. 

Perczel, A., W. Viviani, and I. G. Csizmadia. 1992. Peptide Conformational Potential Energy Surfaces and Their Relevance to Protein Folding in Molecular Aspects of Biotechnology Computational Models and Theories, Bertran, J., ed., Kluwer Academic Publishers, 39-82. 

Figure 13 A typical one-dimensional potential energy surface for a chemical reaction. Two stable states corresponding to the reactants A and the products B are separated by a barrier. The transition between the two states is described by a reaction coordinate q that takes on different values for the reactants and products. The rate-limiting step corresponds to reaching the conformation located at the top of the barrier qf which is the transition state. Depending on the namre of the underlying dynamical process, the rate of the reaction can be predicted accurately by one transition state theory or the Kramers formalism. In protein folding, the reactants A are associated with the unfolded state and the products B are taken to be the folded native state. The reaction coordinate typically remains unspecified. ...

The calculation of the energy or the fitting of the test sequence in the fold of the template is no easy matter. The utilization of a full force field with complete atom representation does not properly discriminate between the different folds [31]. This seems to be related to an energy surface that is too fine and the presence of numerous local minima. In its place a potential function based on a statistical analysis of known protein structures has been developed [34], The pair-wise penalty function provides a pseudo-energy based on the number of times the specific interaction has been observed in known protein structures. This function provides amino acid-amino acid interactions as well as a measure for the solvent exposure of each amino acid [34],... 

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