By Ying Xu, Dong Xu, Jie Liang
Quantity one in every of this two-volume series specializes in the elemental characterization of identified protein buildings, and constitution prediction from protein series info. 11 chapters survey of the sphere, protecting key issues in modeling, strength fields, class, computational tools, and constitution prediction. every one bankruptcy is a self contained assessment overlaying definition of the matter and historic viewpoint; mathematical formula; computational equipment and algorithms; functionality effects; latest software program; strengths, pitfalls, demanding situations, and destiny research.
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Extra info for Computational Methods for Protein Structure Prediction and Modeling: Volume 1: Basic Characterization (Biological and Medical Physics, Biomedical Engineering)
2004). The efficiency of using comparative modeling will be determined by the advances of distant homology detection and fold recognition algorithms, while the efficiency of using ab initio methods will be largely determined by the improvement of the quality of models and the reduction in computing time. Predictions done through comparative modeling and ab initio methods can compensate each other and thus play a particularly important role for structural SVNY330-Xu-Vol-I November 2, 2006 16:58 30 John C.
An explosion of joint EM/crystallographic studies in the mid-1990s followed the development of strategies for generating pseudo-atomic-resolution models of macromolecular complexes by combining the data from high-resolution structures of components with lower-resolution EM data for the entire complex (Baker and Johnson, 1996). Electron cryomicroscopy (cryo-EM) can image complexes in their physiological environment and does not require large quantities of the sample. Cryo-EM also provides a means of visualizing the membrane proteins in situ, as opposed to the usually artificial hydrophobic environments used for crystallizing membrane proteins.
Three steps are involved in this algorithm to predict the structure of a protein sequence: a dissection into fragments and the assignment of their structures; the assembly of the fragments into an overall structure of the protein sequence; and the prediction of the spatial arrangement of the assigned structures and then the completion and refinement of highly ranked predicted arrangements. The combinatorial assembly of domains is formulated as the problem of finding the spanning tree in a graph (where each substructure is a vertex, and an SVNY330-Xu-Vol-I November 2, 2006 16:58 1.