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  • 1
    ISSN: 1573-4943
    Keywords: Protein folding ; genetic algorithm ; lattice model ; optimization ; orthogonal array
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We have applied the orthogonal array method to optimize the parameters in the genetic algorithm of the protein folding problem. Our study employed a 210-type lattice model to describe proteins, where the orientation of a residue relative to its neighboring residue is described by two angles. The statistical analysis and graphic representation show that the two angles characterize protein conformations effectively. Our energy function includes a repulsive energy, an energy for the secondary structure preference, and a pairwise contact potential. We used orthogonal array to optimize the parameters of the population, mating factor, mutation factor, and selection factor in the genetic algorithm. By designing an orthogonal set of trials with representative combinations of these parameters, we efficiently determined the optimal set of parameters through a hierarchical search. The optimal parameters were obtained from the protein crambin and applied to the structure prediction of cytochrome B562. The results indicate that the genetic algorithm with the optimal parameters reduces the computing time to reach a converged energy compared to nonoptimal parameters. It also has less chance to be trapped in a local energy minimum, and predicts a protein structure which is closer to the experimental one. Our method may also be applicable to many other optimization problems in computational biology.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Plant ecology 149 (2000), S. 195-205 
    ISSN: 1573-5052
    Keywords: Beijing ; Cluster analysis ; Donglingshan Mountain ; Landscape classification ; Spatial neighboring ; TWINSPAN
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Two methods were employed to find spatial regularity in a complicated mountain landscape of Beijing, China on the basis of functional and structural affinities. The first approach applied Affinity Analysis based on species composition to landscape. The mosaic diversity of the landscape was 3.5298〉3, which means the study landscape is complex and controlled by multiple environmental gradients. These landscape types were divided into 3 parts according to the mean affinity values of 0.2143 and 0.7857 (0.5±1 SD). Modal sites are the central types of the landscape, which include a zonal broad-leaved forest of the region and a conifer plantation replacing the former. Outliers are found in the highest altitude and the lowest, both have few species in common with the above two modal types. The remaining landscape types are intermediate sites, which are transitional between modals and outliers, broadly distributed throughout mountain environments. Neighbor types have more species in common than those more widely separated, which probably distributed adjacently in space or in similar quality habitat. The other method employed is the new TWINSPAN analysis by substituting spatial neighboring data of landscape types for species composition data. It clearly divided the landscape types into three groups, i.e., subalpine, middle and low mountain groups, which were correlated with altitude, as well as influenced by human disturbance. The new TWINSPAN classification method is more reliable in finding spatial gradient of patchy landscapes than affinity analysis; however, affinity analysis is useful in finding species diversity pattern and the importance of landscape types in a region. Integrating advantages of the two methods could supply complete and reliable information on how landscape types are distributed in space, which environmental gradient dominates the spatial distribution of the landscape types, as well as where important and unusual types are located.
    Type of Medium: Electronic Resource
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