A Spatial Indexing Approach for Protein Structure Modeling
ABSTRACT This paper explores the use of spatial indices for the modeling and retrieval of protein structures. With two existing spatial indices, a preliminary framework for protein structure modeling that uses a spatial index is proposed. It provides a novel technique for modeling. In addition, it provides additional flexibility with respect to modeling granularity and structure manipulation. It is expected that this modeling approach will lead to new ways of analyzing protein structures.
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Article: The Ubiquitous B-Tree.ACM Comput. Surv. 01/1979; 11:121-137.
Article: Multidimensional Access Methods[show abstract] [hide abstract]
ABSTRACT: Search operations in databases require some special support at the physical level. This is true for conventional databases as well as for spatial databases, where typical search operations include the point query (find all objects that contain a given search point) and the region query (find all objects that overlap a given search region). More than ten years of spatial database research have resulted in a great variety of multidimensional access methods to support such operations. This paper gives an overview of that work. After a brief survey of spatial data management in general, we first present the class of point access methods, which are used to search sets of points in two or more dimensions. The second part of the paper is devoted to spatial access methods, which are able to manage extended objects (such as rectangles or polyhedra). We conclude with a discussion of theoretical and experimental results concerning the relative performance of the various approaches. Ke...07/1999;
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ABSTRACT: Examination of a protein's structural 'neighbors' can reveal distant evolutionary relationships that are otherwise undetectable, and perhaps suggest unsuspected functional properties. In the past, such analyses have often required specialized software and computer skills, but new structural comparison methods, developed in the past two years, increasingly offer this opportunity to structural and molecular biologists in general. These methods are based on similarity-search algorithms that are fast enough to have effectively removed the computer-time limitation for structure-structure search and alignment, and have made it possible for several groups to conduct systematic comparisons of all publicly available structures, and offer this information via the World Wide Web. Furthermore, and perhaps surprisingly given the difficulty of the structure-comparison problem, these groups seem to have converged on quite similar approaches with respect to both fast search algorithms and the identification of statistically significant similarities.Current Opinion in Structural Biology 07/1996; 6(3):377-85. · 8.74 Impact Factor