TM-search: An Efficient and Effective Tool for Protein Structure Database Search.
J Chem Inf Model
; 64(3): 1043-1049, 2024 Feb 12.
Article
em En
| MEDLINE
| ID: mdl-38270339
ABSTRACT
The quickly increasing size of the Protein Data Bank is challenging biologists to develop a more scalable protein structure alignment tool for fast structure database search. Although many protein structure search algorithms and programs have been designed and implemented for this purpose, most require a large amount of computational time. We propose a novel protein structure search approach, TM-search, which is based on the pairwise structure alignment program TM-align and a new iterative clustering algorithm. Benchmark tests demonstrate that TM-search is 27 times faster than a TM-align full database search while still being able to identify â¼90% of all high TM-score hits, which is 2-10 times more than other existing programs such as Foldseek, Dali, and PSI-BLAST.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Proteínas
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
J Chem Inf Model
Assunto da revista:
INFORMATICA MEDICA
/
QUIMICA
Ano de publicação:
2024
Tipo de documento:
Article
País de afiliação:
China