K.A. Dill, A.T. Phillips, and J.B. Rosen, Molecular Structure Prediction by Global Optimization,  Home/Search   Document Details and Download   Summary   Related Articles   Check

.... and bond angles are discussed in Kostrowicki Scheraga [174] Similar techniques for smoothing have been proposed and applied to potential energy surfaces by Coleman et al. 55] More e Wu [214, 215] Shalloway [283] and Wu [349] A different smoothing technique is proposed in Dill et al. [79]. They construct a surrogate potential surface by fitting an underestimating function to known local optima, hoping that the global optimum lies near the minimizer of this surrogate function. A kind of hybrid method between simulated annealing and smoothing is the quantum mechanical annealing ....

....al. 289] for lysozyme, myoglobin and thymosin. In all these papers, results are only native like when compared with the experimental structures. Related techniques based on backbone models with terms involving information from Ramachandran plots (see next section) are discussed in Dill et al. [79]. As in earlier models (e.g. Honeycutt Thirumalai [146] the amino acids are treated in a reduced descriprion only, based on their hydrophilic or hydrophobic affinity. Lattice models with contact potentials. Here the molecule is forced to have its atoms lying on lattice positions, and the ....

K. A. Dill, A. T. Phillips and J. B. Rosen, Molecular structure prediction by global optimization, Manuscript (1996). (phillips@nadn.navy.mil)

....ex , E hp , and E jy ) where f R t with t=2n 2 in place of n 1. Computational testing of the CGU algorithm using this new detailed polypeptide model with the Sun Thomas Dill potential energy function on actual protein sequences is presented in the separate paper by Dill, Phillips, and Rosen [2]. 6. Conclusions Preliminary computational testing of the CGU algorithm applied to a simplified polypeptide model has demonstrated that the method is practical for both the homopolymer and heteropolymer models and for sequences with as many as 48 monomers. Furthermore, since the CGU algorithm is ....

K.A. Dill, A.T. Phillips, and J.B. Rosen, Molecular Structure Prediction by Global Optimization,

....for another quadratic underestimation over the reduced space. After several repetitions, the global minimum conformation f G and its associated global minimum energy F(f G ) can be found with reasonable assurance. For more specific details of the CGU method and its computational results, see [2] [3], 4] and [6] 3. Global Underestimation of the Energy Landscape As summarized in the previous section, the CGU algorithm will determine a global minimum backbone torsion angle vector f G and corresponding global minimum energy function value F G = F(f G ) As part of the CGU algorithm, a ....

....PROTEIN STRUCTURE AND ENERGY LANDSCAPE DEPENDENCE ON SEQUENCE 11 many local minima and the energy gap between the global minimum and all others is significant. Finally, based on the computational results obtained so far, the average running time, as a function of peptide length n, is O(n 4 ) [3]. This function has been com Figure 5 CGU Computed Structure for 7ZNF Figure 6 Ball and Stick Representation of the CGU Computed Structure for 7ZNF PROTEIN STRUCTURE AND ENERGY LANDSCAPE DEPENDENCE ON SEQUENCE 12 puted (based on the results presented in both this and the next section) to be ....

K.A. Dill, A.T. Phillips, and J.B. Rosen, Molecular Structure Prediction by Global Optimization, Developments in Global Optimization (1997), I.M. Bomze et al. (Eds), 217-234.

....of the twenty individual amino acids, parameterized from the Protein Databank. Since the CGU method re 8 quires a differentiable potential function (in order to apply our continuous minimization method) we approximate the discrete Ramachandran map data by a continuous function of OE and (see [11] for complete details) However, the CGU search method is still quite general; it depends neither on the level of detail of the molecular model nor on the functional forms of the energy terms F i (OE) The following evidence suggests that the CGU method is a successful search strategy: 1. Having ....

Dill, K.A., A.T. Phillips, and J.B. Rosen (1997), Molecular structure prediction by global optimization, Developments in Global Optimization, 217234, I.M. Bomze et al. (Eds).

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