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Aligning EM density maps and fitting atomic models are essential steps in single particle cryogenic electron microscopy (cryo-EM), with recent methods leveraging various algorithms and machine learning tools.
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A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps
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Rigid-body fitting of atomic models on 3D density maps of electron microscopy
Kawabata T · 2018
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Kawabata T · 2018
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Advances in structure modeling methods for cryo-electron microscopy maps
Alnabati E, Kihara D · 2019
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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
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State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps
Zhang Y, Krieger J, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, et al · 2020
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MorphOT: Transport-based interpolation between EM maps with UCSF ChimeraX
Ecoffet A, Poitevin F, Dao Duc K · 2020
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Earthmover-based manifold learning for analyzing molecular conformation spaces
Zelesko N, Moscovich A, Kileel J, Singer A · 2020
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Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al · 2021
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Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, et al · 2021
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Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, et al · 2021
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AlignOT: An optimal transport based algorithm for fast 3D alignment with applications to cryogenic electron microscopy density maps
Riahi AT, Woollard G, Poitevin F, Condon A, Duc KD · 2022
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Progressive assembly of multi-domain protein structures from cryo-EM density maps
Zhou X, Li Y, Zhang C, Zheng W, Zhang G, Zhang Y · 2022
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Wasserstein k-means for clustering tomographic projections
Rao R, Moscovich A, Singer A · 2020
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VESPER: global and local cryo-EM map alignment using local density vectors
Han X, Terashi G, Christoffer C, Chen S, Kihara D · 2021
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DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes
Pfab J, Phan NM, Si D · 2021
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The unbalanced gromov wasserstein distance: Conic formulation and relaxation
Séjourné T, Vialard FX, Peyré G · 2021
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Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly
He J, Lin P, Chen J, Cao H, Huang SY · 2022
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Application of transport-based metric for continuous interpolation between cryo-EM density maps
Ecoffet A, Woollard G, Kushner A, Poitevin F, Dao Duc K · 2022
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Three-dimensional alignment of density maps in cryo-electron microscopy
Harpaz Y, Shkolnisky Y · 2023
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Alignment of Density Maps in Wasserstein Distance
Singer A, Yang R · 2023
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