Explore Protein Conformational Space With Variational Autoencoder

Molecular dynamics (MD) simulations have been actively used in the study of protein structure and function. However, extensive sampling in the protein conformational space requires large computational resources and takes a prohibitive amount of time. In this study, we demonstrated that variational a...

Descripción completa

Guardado en:
Detalles Bibliográficos
Autores principales: Hao Tian, Xi Jiang, Francesco Trozzi, Sian Xiao, Eric C. Larson, Peng Tao
Formato: article
Lenguaje:EN
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://doaj.org/article/0dd63e9213564b10acf17ca8968be3b0
Etiquetas: Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
Descripción
Sumario:Molecular dynamics (MD) simulations have been actively used in the study of protein structure and function. However, extensive sampling in the protein conformational space requires large computational resources and takes a prohibitive amount of time. In this study, we demonstrated that variational autoencoders (VAEs), a type of deep learning model, can be employed to explore the conformational space of a protein through MD simulations. VAEs are shown to be superior to autoencoders (AEs) through a benchmark study, with low deviation between the training and decoded conformations. Moreover, we show that the learned latent space in the VAE can be used to generate unsampled protein conformations. Additional simulations starting from these generated conformations accelerated the sampling process and explored hidden spaces in the conformational landscape.