A Method of Structure Comparison Using Spatial Topological Patterns

2005 ◽  
Vol 277-279 ◽  
pp. 272-277
Author(s):  
Sung Hee Park ◽  
Keun Ho Ryu
Keyword(s):  
Spatial Data ◽  
Similarity Search ◽  
3D Structure ◽  
Structural Similarity ◽  
Query Protein ◽  
Data Types ◽  
Structure Comparison ◽  
3D Space ◽  
Structure Databases ◽  
Computationally Expensive

The problem of comparison of structural similarity has been complex and computationally expensive. The first step to solve comparison of structural similarity in 3D structure databases is to develop fast methods for structural similarity. Therefore, we propose a new method of comparing structural similarity in protein structure databases by using topological patterns of proteins. In our approach, the geometry of secondary structure elements in 3D space is represented by spatial data types and is indexed using Rtrees. Topological patterns are discovered by spatial topology relations based on the Rtree index join. An algorithm for a similarity search compares topological patterns of a query protein with those of proteins in structure databases by the intersection frequency of SSEs. Our experimental results show that the execution time of our method is three times faster than the generally known method DALITE. Our method can generate small candidate sets for more accurate alignment tools such as DALI and SSAP.

scholarly journals CoeViz 2: Protein Graphs Derived From Amino Acid Covariance

2021 ◽  
Vol 1 ◽  
Author(s):  
Daniel Corcoran ◽  
Nicholas Maltbie ◽  
Shivchander Sudalairaj ◽  
Frazier N. Baker ◽  
Joseph Hirschfeld ◽  
...  
Keyword(s):  
Metal Binding ◽  
Large Scale ◽  
Pearson Correlation ◽  
3D Structure ◽  
Covariance Analysis ◽  
Web Based ◽  
Functional Sites ◽  
3D Space ◽  
Chi Squared ◽  
Molecular Functions

Proteins by and large carry out their molecular functions in a folded state when residues, distant in sequence, assemble together in 3D space to bind a ligand, catalyze a reaction, form a channel, or exert another concerted macromolecular interaction. It has been long recognized that covariance of amino acids between distant positions within a protein sequence allows for the inference of long range contacts to facilitate 3D structure modeling. In this work, we investigated whether covariance analysis may reveal residues involved in the same molecular function. Building upon our previous work, CoeViz, we have conducted a large scale covariance analysis among 7,595 non-redundant proteins with resolved 3D structures to assess 1) whether the residues with the same function coevolve, 2) which covariance metric captures such couplings better, and 3) how different molecular functions compare in this context. We found that the chi-squared metric is the most informative for the identification of coevolving functional sites, followed by the Pearson correlation-based, whereas mutual information is the least informative. Of the seven categories of the most common natural ligands, including coenzyme A, dinucleotide, DNA/RNA, heme, metal, nucleoside, and sugar, the trace metal binding residues display the most prominent coupling, followed by the sugar binding sites. We also developed a web-based tool, CoeViz 2, that enables the interactive visualization of covarying residues as cliques from a larger protein graph. CoeViz 2 is publicly available at https://research.cchmc.org/CoevLab/.

Object-Relational Spatial Indexing

2011 ◽  
pp. 49-80
Author(s):  
Hans-Peter Kriegel ◽  
Martin Pfeifle ◽  
Marco Potke ◽  
Thomas Seidl ◽  
Jost Enderle
Keyword(s):  
Spatial Data ◽  
Concurrency Control ◽  
Buffer Management ◽  
Database Systems ◽  
Data Types ◽  
Spatial Access ◽  
Access Methods ◽  
Object Relational ◽  
Relational Database Systems ◽  
Spatial Access Methods

In order to generate efficient execution plans for queries comprising spatial data types and predicates, the database system has to be equipped with appropriate index structures, query processing methods and optimization rules. Although available extensible indexing frameworks provide a gateway for seamless integration of spatial access methods into the standard process of query optimization and execution, they do not facilitate the actual implementation of the spatial access method. An internal enhancement of the database kernel is usually not an option for database developers. The embedding of a custom, block-oriented index structure into concurrency control, recovery services and buffer management would cause extensive implementation efforts and maintenance cost, at the risk of weakening the reliability of the entire system. The server stability can be preserved by delegating index operations to an external process, but this approach induces severe performance bottlenecks due to context switches and inter-process communication. Therefore, we present the paradigm of object-relational spatial access methods that perfectly fits to the common relational data model, and is highly compatible with the extensible indexing frameworks of existing object-relational database systems, allowing the user to define application-specific access methods.

The Integral of Spatial Data Mining in the Era of Big Data

2017 ◽  
pp. 90-126
Author(s):  
Gebeyehu Belay Gebremeskel ◽  
Chai Yi ◽  
Zhongshi He
Keyword(s):  
Data Mining ◽  
Data Warehouse ◽  
Spatial Data ◽  
High Volume ◽  
Spatial Data Mining ◽  
Research Field ◽  
Data Sets ◽  
Data Types ◽  
Basic Principles ◽  
Gis Data

Data Mining (DM) is a rapidly expanding field in many disciplines, and it is greatly inspiring to analyze massive data types, which includes geospatial, image and other forms of data sets. Such the fast growths of data characterized as high volume, velocity, variety, variability, value and others that collected and generated from various sources that are too complex and big to capturing, storing, and analyzing and challenging to traditional tools. The SDM is, therefore, the process of searching and discovering valuable information and knowledge in large volumes of spatial data, which draws basic principles from concepts in databases, machine learning, statistics, pattern recognition and 'soft' computing. Using DM techniques enables a more efficient use of the data warehouse. It is thus becoming an emerging research field in Geosciences because of the increasing amount of data, which lead to new promising applications. The integral SDM in which we focused in this chapter is the inference to geospatial and GIS data.

Spatial and Spatiotemporal Data Types as a Foundation for Representing Space-Time Data in GIS

2017 ◽  
pp. 1-28 ◽  
Author(s):  
Markus Schneider
Keyword(s):  
Spatial Data ◽  
Geographical Information Systems ◽  
Moving Objects ◽  
Spatial Databases ◽  
Query Languages ◽  
Geographical Information ◽  
Spatiotemporal Data ◽  
Data Types ◽  
Time Data ◽  
Use Of Data

A data type comprises a set of homogeneous values together with a collection of operations defined on them. This chapter emphasizes the importance of crisp spatial data types, fuzzy spatial data types, and spatiotemporal data types for representing static, vague, and time-varying geometries in Geographical Information Systems (GIS). These data types provide a fundamental abstraction for modeling the geometric structure of crisp spatial, fuzzy spatial, and moving objects in space and time as well as their relationships, properties, and operations. The goal of this chapter is to provide an overview and description of these data types and their operations that have been proposed in research and can be found in GIS, spatial databases, moving objects databases, and other spatial software tools. The use of data types, operations, and predicates will be illustrated by their embedding into query languages.

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