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For: Cossio P, Hummer G. Likelihood-based structural analysis of electron microscopy images. Curr Opin Struct Biol 2018;49:162-168. [PMID: 29579548 DOI: 10.1016/j.sbi.2018.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/24/2018] [Accepted: 03/06/2018] [Indexed: 10/17/2022]
Number Cited by Other Article(s)
1
Tang WS, Zhong ED, Hanson SM, Thiede EH, Cossio P. Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy. Curr Opin Struct Biol 2023;81:102626. [PMID: 37311334 DOI: 10.1016/j.sbi.2023.102626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/25/2023] [Accepted: 05/16/2023] [Indexed: 06/15/2023]
2
Toader B, Sigworth FJ, Lederman RR. Methods for Cryo-EM Single Particle Reconstruction of Macromolecules Having Continuous Heterogeneity. J Mol Biol 2023;435:168020. [PMID: 36863660 PMCID: PMC10164696 DOI: 10.1016/j.jmb.2023.168020] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/02/2023]
3
DeVore K, Chiu PL. Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity. Biomolecules 2022;12:biom12050628. [PMID: 35625556 PMCID: PMC9138638 DOI: 10.3390/biom12050628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023]  Open
4
Wälti MA, Canagarajah B, Schwieters CD, Clore GM. Visualization of Sparsely-populated Lower-order Oligomeric States of Human Mitochondrial Hsp60 by Cryo-electron Microscopy. J Mol Biol 2021;433:167322. [PMID: 34688687 PMCID: PMC8627483 DOI: 10.1016/j.jmb.2021.167322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/19/2022]
5
Giraldo-Barreto J, Ortiz S, Thiede EH, Palacio-Rodriguez K, Carpenter B, Barnett AH, Cossio P. A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments. Sci Rep 2021;11:13657. [PMID: 34211017 PMCID: PMC8249403 DOI: 10.1038/s41598-021-92621-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/01/2021] [Indexed: 11/08/2022]  Open
6
Zhang Y, Krieger J, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I. State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021;160:104-120. [PMID: 32866476 PMCID: PMC7914283 DOI: 10.1016/j.pbiomolbio.2020.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/25/2020] [Accepted: 08/16/2020] [Indexed: 12/17/2022]
7
Zhang J, Wang Z, Liu Z, Zhang F. Improve the Resolution and Parallel Performance of the Three-Dimensional Refine Algorithm in RELION Using CUDA and MPI. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:583-595. [PMID: 31329127 DOI: 10.1109/tcbb.2019.2929171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
8
Ortiz S, Stanisic L, Rodriguez BA, Rampp M, Hummer G, Cossio P. Validation tests for cryo-EM maps using an independent particle set. J Struct Biol X 2020;4:100032. [PMID: 32743544 PMCID: PMC7385033 DOI: 10.1016/j.yjsbx.2020.100032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
9
Cossio P. Need for Cross-Validation of Single Particle Cryo-EM. J Chem Inf Model 2020;60:2413-2418. [PMID: 32101412 DOI: 10.1021/acs.jcim.9b01121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
10
Harastani M, Sorzano COS, Jonić S. Hybrid Electron Microscopy Normal Mode Analysis with Scipion. Protein Sci 2019;29:223-236. [PMID: 31693263 DOI: 10.1002/pro.3772] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
11
Bonomi M, Vendruscolo M. Determination of protein structural ensembles using cryo-electron microscopy. Curr Opin Struct Biol 2019;56:37-45. [DOI: 10.1016/j.sbi.2018.10.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/24/2018] [Accepted: 10/26/2018] [Indexed: 10/27/2022]
12
Köfinger J, Różycki B, Hummer G. Inferring Structural Ensembles of Flexible and Dynamic Macromolecules Using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods. Methods Mol Biol 2019;2022:341-352. [PMID: 31396910 DOI: 10.1007/978-1-4939-9608-7_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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