Enhancing Protein Function Prediction Performance by Utilizing AlphaFold-Predicted Protein Structures.
J Chem Inf Model
; 62(17): 4008-4017, 2022 09 12.
Article
em En
| MEDLINE
| ID: mdl-36006049
ABSTRACT
The structure of a protein is of great importance in determining its functionality, and this characteristic can be leveraged to train data-driven prediction models. However, the limited number of available protein structures severely limits the performance of these models. AlphaFold2 and its open-source data set of predicted protein structures have provided a promising solution to this problem, and these predicted structures are expected to benefit the model performance by increasing the number of training samples. In this work, we constructed a new data set that acted as a benchmark and implemented a state-of-the-art structure-based approach for determining whether the performance of the function prediction model can be improved by putting additional AlphaFold-predicted structures into the training set and further compared the performance differences between two models separately trained with real structures only and AlphaFold-predicted structures only. Experimental results indicated that structure-based protein function prediction models could benefit from virtual training data consisting of AlphaFold-predicted structures. First, model performances were improved in all three categories of Gene Ontology terms (GO terms) after adding predicted structures as training samples. Second, the model trained only on AlphaFold-predicted virtual samples achieved comparable performances to the model based on experimentally solved real structures, suggesting that predicted structures were almost equally effective in predicting protein functionality.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Proteínas
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
J Chem Inf Model
Assunto da revista:
INFORMATICA MEDICA
/
QUIMICA
Ano de publicação:
2022
Tipo de documento:
Article
País de afiliação:
China