{"title":"Assessments of Variational Autoencoder in Protein Conformation Exploration.","authors":"Sian Xiao, Zilin Song, Hao Tian, Peng Tao","doi":"10.1142/s2737416523500217","DOIUrl":null,"url":null,"abstract":"<p><p>Molecular dynamics (MD) simulations have been extensively used to study protein dynamics and subsequently functions. However, MD simulations are often insufficient to explore adequate conformational space for protein functions within reachable timescales. Accordingly, many enhanced sampling methods, including variational autoencoder (VAE) based methods, have been developed to address this issue. The purpose of this study is to evaluate the feasibility of using VAE to assist in the exploration of protein conformational landscapes. Using three modeling systems, we showed that VAE could capture high-level hidden information which distinguishes protein conformations. These models could also be used to generate new physically plausible protein conformations for direct sampling in favorable conformational spaces. We also found that VAE worked better in interpolation than extrapolation and increasing latent space dimension could lead to a trade-off between performances and complexities.</p>","PeriodicalId":2,"journal":{"name":"ACS Applied Bio Materials","volume":" ","pages":"489-501"},"PeriodicalIF":4.6000,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11138204/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"ACS Applied Bio Materials","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1142/s2737416523500217","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2023/3/27 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"MATERIALS SCIENCE, BIOMATERIALS","Score":null,"Total":0}
引用次数: 0
Abstract
Molecular dynamics (MD) simulations have been extensively used to study protein dynamics and subsequently functions. However, MD simulations are often insufficient to explore adequate conformational space for protein functions within reachable timescales. Accordingly, many enhanced sampling methods, including variational autoencoder (VAE) based methods, have been developed to address this issue. The purpose of this study is to evaluate the feasibility of using VAE to assist in the exploration of protein conformational landscapes. Using three modeling systems, we showed that VAE could capture high-level hidden information which distinguishes protein conformations. These models could also be used to generate new physically plausible protein conformations for direct sampling in favorable conformational spaces. We also found that VAE worked better in interpolation than extrapolation and increasing latent space dimension could lead to a trade-off between performances and complexities.
期刊介绍:
ACS Applied Bio Materials is an interdisciplinary journal publishing original research covering all aspects of biomaterials and biointerfaces including and beyond the traditional biosensing, biomedical and therapeutic applications.
The journal is devoted to reports of new and original experimental and theoretical research of an applied nature that integrates knowledge in the areas of materials, engineering, physics, bioscience, and chemistry into important bio applications. The journal is specifically interested in work that addresses the relationship between structure and function and assesses the stability and degradation of materials under relevant environmental and biological conditions.