Enhancing cryo-EM structure prediction with DeepTracer and AlphaFold2 integration

• Published in: Briefings in bioinformatics Vol. 25; no. 3
• Main Authors: Chen, Jason, Zia, Ayisha, Luo, Albert, Meng, Hanze, Wang, Fengbin, Hou, Jie, Cao, Renzhi, Si, Dong
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 27.03.2024; Oxford Publishing Limited (England)
• Subjects: Amino Acid Sequence; Automation; Biological Evolution; Biomedical materials; Cryoelectron Microscopy; Databases, Factual; Electron density; Electron microscopy; Labor; Learning algorithms; Machine Learning; Protein structure; Proteins; Structures; Vaccine development; protein structure; refinement; DeepTracer; protein docking; cryo-EM; AlphaFold
• ISSN: 1467-5463; 1477-4054
• DOI: 10.1093/bib/bbae118

Abstract Understanding the protein structures is invaluable in various biomedical applications, such as vaccine development. Protein structure model building from experimental electron density maps is a time-consuming and labor-intensive task. To address the challenge, machine learning approaches have been proposed to automate this process. Currently, the majority of the experimental maps in the database lack atomic resolution features, making it challenging for machine learning-based methods to precisely determine protein structures from cryogenic electron microscopy density maps. On the other hand, protein structure prediction methods, such as AlphaFold2, leverage evolutionary information from protein sequences and have recently achieved groundbreaking accuracy. However, these methods often require manual refinement, which is labor intensive and time consuming. In this study, we present DeepTracer-Refine, an automated method that refines AlphaFold predicted structures by aligning them to DeepTracers modeled structure. Our method was evaluated on 39 multi-domain proteins and we improved the average residue coverage from 78.2 to 90.0% and average local Distance Difference Test score from 0.67 to 0.71. We also compared DeepTracer-Refine with Phenixs AlphaFold refinement and demonstrated that our method not only performs better when the initial AlphaFold model is less precise but also surpasses Phenix in run-time performance.