An optimized relational database for querying structural patterns in proteins-Reference-Cited by-同舟云学术

An optimized relational database for querying structural patterns in proteins

Published:2023-01-01 Issue: Volume:2024 Page:
ISSN:1758-0463
Container-title:Database
language:en
Short-container-title:

Author:

Angles Renzo¹²^ORCID,Arenas-Salinas Mauricio³^ORCID,García Roberto²⁴^ORCID,Ingram Ben⁵^ORCID

Affiliation:

1. Department of Computer Science, Faculty of Engineering, Universidad de Talca , Camino a Los Niches Km. 1, Curicó, Región del Maule 3340000, Chile

2. Millennium Institute for Foundational Research on Data (IMFD) , Vicuña Mackenna 4860, Macul, Santiago, Región Metropolitana 7810000, Chile

3. Centro de Bioinformática y Simulación Molecular (CBSM), Faculty of Engineering, Universidad de Talca , Av. Lircay s/n, Talca Región del Maule 34600000, Chile

4. Engineering Systems Doctoral Program, Faculty of Engineering, Universidad de Talca , Camino a Los Niches Km 1, Curicó, Región del Maule 3340000, Chile

5. School of Water, Energy and Environment, Cranfield University , College Road, Cranfield, Bedfordshire MK43 0AL, England

Abstract

Abstract A database is an essential component in almost any software system, and its creation involves more than just data modeling and schema design. It also includes query optimization and tuning. This paper focuses on a web system called GSP4PDB, which is used for searching structural patterns in proteins. The system utilizes a normalized relational database, which has proven to be inefficient even for simple queries. This article discusses the optimization of the GSP4PDB database by implementing two techniques: denormalization and indexing. The empirical evaluation described in the article shows that combining these techniques enhances the efficiency of the database when querying both real and artificial graph–based structural patterns.

Publisher

Oxford University Press (OUP)

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,Information Systems

Link

https://academic.oup.com/database/article-pdf/doi/10.1093/database/baad093/56206892/baad093.pdf

Reference39 articles.

1. PGR: a novel graph repository of protein 3D-structures;Dhifli Abdoulaye;J. Data Mining in Genomics & Proteomics,2015

2. GSP4PDB: A web tool to visualize, search and explore protein-ligand structural patterns;Angles;BMC Bioinform.,2020

3. RPDB: A relational databank of protein structures;Aslam;Pak. J. Agric. Sci.,2016