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Abstract ChemMLis an open machine learning (ML) and informatics program suite that is designed to support and advance the data‐driven research paradigm that is currently emerging in the chemical and materials domain.ChemMLallows its users to perform various data science tasks and execute ML workflows that are adapted specifically for the chemical and materials context. Key features are automation, general‐purpose utility, versatility, and user‐friendliness in order to make the application of modern data science a viable and widely accessible proposition in the broader chemistry and materials community.ChemMLis also designed to facilitate methodological innovation, and it is one of the cornerstones of the software ecosystem for data‐driven in silico research. This article is categorized under:Software > Simulation MethodsComputer and Information Science > ChemoinformaticsStructure and Mechanism > Computational Materials ScienceSoftware > Molecular Modeling
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Artificial intelligence advances for de novo molecular structure modeling in cryo‐electron microscopy
Abstract Cryo‐electron microscopy (cryo‐EM) has become a major experimental technique to determine the structures of large protein complexes and molecular assemblies, as evidenced by the 2017 Nobel Prize. Although cryo‐EM has been drastically improved to generate high‐resolution three‐dimensional maps that contain detailed structural information about macromolecules, the computational methods for using the data to automatically build structure models are lagging far behind. The traditional cryo‐EM model building approach is template‐based homology modeling. Manual de novo modeling is very time‐consuming when no template model is found in the database. In recent years, de novo cryo‐EM modeling using machine learning (ML) and deep learning (DL) has ranked among the top‐performing methods in macromolecular structure modeling. DL‐based de novo cryo‐EM modeling is an important application of artificial intelligence, with impressive results and great potential for the next generation of molecular biomedicine. Accordingly, we systematically review the representative ML/DL‐based de novo cryo‐EM modeling methods. Their significances are discussed from both practical and methodological viewpoints. We also briefly describe the background of cryo‐EM data processing workflow. Overall, this review provides an introductory guide to modern research on artificial intelligence for de novo molecular structure modeling and future directions in this emerging field. This article is categorized under:Structure and Mechanism > Molecular StructuresStructure and Mechanism > Computational Biochemistry and BiophysicsData Science > Artificial Intelligence/Machine Learning
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- Award ID(s):
- 2030381
- PAR ID:
- 10363811
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- WIREs Computational Molecular Science
- Volume:
- 12
- Issue:
- 2
- ISSN:
- 1759-0876
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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