PSAC-PDB: Analysis and classification of protein structures.
Comput Biol Med
; 158: 106814, 2023 05.
Artigo
em Inglês
| MEDLINE | ID: covidwho-2273828
ABSTRACT
This paper presents a novel framework, called PSAC-PDB, for analyzing and classifying protein structures from the Protein Data Bank (PDB). PSAC-PDB first finds, analyze and identifies protein structures in PDB that are similar to a protein structure of interest using a protein structure comparison tool. Second, the amino acids (AA) sequences of identified protein structures (obtained from PDB), their aligned amino acids (AAA) and aligned secondary structure elements (ASSE) (obtained by structural alignment), and frequent AA (FAA) patterns (discovered by sequential pattern mining), are used for the reliable detection/classification of protein structures. Eleven classifiers are used and their performance is compared using six evaluation metrics. Results show that three classifiers perform well on overall, and that FAA patterns can be used to efficiently classify protein structures in place of providing the whole AA sequences, AAA or ASSE. Furthermore, better classification results are obtained using AAA of protein structures rather than AA sequences. PSAC-PDB also performed better than state-of-the-art approaches for SARS-CoV-2 genome sequences classification.
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Texto completo:
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Coleções:
Bases de dados internacionais
Base de dados:
MEDLINE
Assunto principal:
COVID-19
Tipo de estudo:
Estudo experimental
Limite:
Humanos
Idioma:
Inglês
Revista:
Comput Biol Med
Ano de publicação:
2023
Tipo de documento:
Artigo
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