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Type
Number of Years Citation(s) in RCA
1
Wang RYR, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife 2016;5. [PMID: 27669148 PMCID: PMC5115868 DOI: 10.7554/elife.17219] [Citation(s) in RCA: 375] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/22/2016] [Indexed: 01/25/2023]  Open
Research Support, N.I.H., Extramural 9 375
2
Cabezón E, Ripoll-Rozada J, Peña A, de la Cruz F, Arechaga I. Towards an integrated model of bacterial conjugation. FEMS Microbiol Rev 2014;39:81-95. [PMID: 25154632 DOI: 10.1111/1574-6976.12085] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
Review 11 127
3
Lasker K, Topf M, Sali A, Wolfson HJ. Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. J Mol Biol 2009;388:180-94. [PMID: 19233204 PMCID: PMC2680734 DOI: 10.1016/j.jmb.2009.02.031] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2008] [Revised: 12/29/2008] [Accepted: 02/12/2009] [Indexed: 11/24/2022]
Research Support, N.I.H., Extramural 16 97
4
Schneidman-Duhovny D, Pellarin R, Sali A. Uncertainty in integrative structural modeling. Curr Opin Struct Biol 2014;28:96-104. [PMID: 25173450 PMCID: PMC4252396 DOI: 10.1016/j.sbi.2014.08.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 07/24/2014] [Accepted: 08/05/2014] [Indexed: 01/08/2023]
Research Support, N.I.H., Extramural 11 81
5
Sousa AA, Leapman RD. Development and application of STEM for the biological sciences. Ultramicroscopy 2012;123:38-49. [PMID: 22749213 PMCID: PMC3500455 DOI: 10.1016/j.ultramic.2012.04.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 04/06/2012] [Accepted: 04/13/2012] [Indexed: 01/06/2023]
Research Support, N.I.H., Intramural 13 54
6
Comprehensive structural model of the mechanochemical cycle of a mitotic motor highlights molecular adaptations in the kinesin family. Proc Natl Acad Sci U S A 2014;111:1837-42. [PMID: 24449904 DOI: 10.1073/pnas.1319848111] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Research Support, Non-U.S. Gov't 11 47
7
Rothnie A, Clarke AR, Kuzmic P, Cameron A, Smith CJ. A sequential mechanism for clathrin cage disassembly by 70-kDa heat-shock cognate protein (Hsc70) and auxilin. Proc Natl Acad Sci U S A 2011;108:6927-32. [PMID: 21482805 PMCID: PMC3084117 DOI: 10.1073/pnas.1018845108] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
research-article 14 46
8
NMR mapping of PCNA interaction with translesion synthesis DNA polymerase Rev1 mediated by Rev1-BRCT domain. J Mol Biol 2013;425:3091-105. [PMID: 23747975 DOI: 10.1016/j.jmb.2013.05.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 05/13/2013] [Accepted: 05/30/2013] [Indexed: 01/13/2023]
Research Support, Non-U.S. Gov't 12 40
9
Braitbard M, Schneidman-Duhovny D, Kalisman N. Integrative Structure Modeling: Overview and Assessment. Annu Rev Biochem 2019;88:113-135. [PMID: 30830798 DOI: 10.1146/annurev-biochem-013118-111429] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Review 6 36
10
Hosseinizadeh A, Schwander P, Dashti A, Fung R, D'Souza RM, Ourmazd A. High-resolution structure of viruses from random diffraction snapshots. Philos Trans R Soc Lond B Biol Sci 2015;369:20130326. [PMID: 24914154 PMCID: PMC4052863 DOI: 10.1098/rstb.2013.0326] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
Research Support, U.S. Gov't, Non-P.H.S. 10 32
11
Beck M, Topf M, Frazier Z, Tjong H, Xu M, Zhang S, Alber F. Exploring the spatial and temporal organization of a cell's proteome. J Struct Biol 2011;173:483-96. [PMID: 21094684 PMCID: PMC3784337 DOI: 10.1016/j.jsb.2010.11.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Revised: 11/05/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
Research Support, N.I.H., Extramural 14 25
12
Dror O, Lasker K, Nussinov R, Wolfson H. EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2007;63:42-9. [PMID: 17164525 PMCID: PMC2483490 DOI: 10.1107/s0907444906041059] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Accepted: 10/08/2006] [Indexed: 11/22/2022]
Research Support, N.I.H., Extramural 18 17
13
Haldrup K. Singular value decomposition as a tool for background corrections in time-resolved XFEL scattering data. Philos Trans R Soc Lond B Biol Sci 2014;369:20130336. [PMID: 24914162 DOI: 10.1098/rstb.2013.0336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
11 14
14
Simon AJ, Walls-Smith LT, Freddi MJ, Fong FY, Gubala V, Plaxco KW. Simultaneous Measurement of the Dissolution Kinetics of Responsive DNA Hydrogels at Multiple Length Scales. ACS NANO 2017;11:461-468. [PMID: 28006092 DOI: 10.1021/acsnano.6b06414] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Research Support, N.I.H., Extramural 8 9
15
Kim EA, Panushka J, Meyer T, Ide N, Carlisle R, Baker S, Blair DF. Biogenesis of the Flagellar Switch Complex in Escherichia coli: Formation of Sub-Complexes Independently of the Basal-Body MS-Ring. J Mol Biol 2017. [PMID: 28625846 DOI: 10.1016/j.jmb.2017.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Journal Article 8 7
16
Kuo J. Metal shadowing for electron microscopy. Methods Mol Biol 2014;1117:73-93. [PMID: 24357360 PMCID: PMC7120032 DOI: 10.1007/978-1-62703-776-1_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
chapter-article 11 6
17
Mathew A, Giskes F, Lekkas A, Greisch JF, Eijkel GB, Anthony IGM, Fort K, Heck AJR, Papanastasiou D, Makarov AA, Ellis SR, Heeren RMA. An Orbitrap/Time-of-Flight Mass Spectrometer for Photofragment Ion Imaging and High-Resolution Mass Analysis of Native Macromolecular Assemblies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37319176 DOI: 10.1021/jasms.3c00053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
2 3
18
Habeck M. Bayesian methods in integrative structure modeling. Biol Chem 2023;404:741-754. [PMID: 37505205 DOI: 10.1515/hsz-2023-0145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023]
Review 2 3
19
Welke RW, Sperber HS, Bergmann R, Koikkarah A, Menke L, Sieben C, Krüger DH, Chiantia S, Herrmann A, Schwarzer R. Characterization of Hantavirus N Protein Intracellular Dynamics and Localization. Viruses 2022;14:v14030457. [PMID: 35336863 PMCID: PMC8954124 DOI: 10.3390/v14030457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 02/02/2022] [Accepted: 02/18/2022] [Indexed: 02/07/2023]  Open
3 3
20
Loquet A, Tolchard J, Berbon M, Martinez D, Habenstein B. Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy. J Vis Exp 2017:55779. [PMID: 28994783 PMCID: PMC5752270 DOI: 10.3791/55779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
Video-Audio Media 8 1
21
Pasani S, Menon KS, Viswanath S. The molecular architecture of the desmosomal outer dense plaque by integrative structural modeling. Protein Sci 2024;33:e5217. [PMID: 39548826 PMCID: PMC11568391 DOI: 10.1002/pro.5217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 10/22/2024] [Accepted: 10/23/2024] [Indexed: 11/18/2024]
research-article 1
22
Alonzo-Velázquez JL, Botello-Rionda S, Herrera-Guzmán R, Carrillo-Tripp M. CapsidMesh: Atomic-detail structured mesh representation of icosahedral viral capsids and the study of their mechanical properties. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2018;34:e2991. [PMID: 29603677 DOI: 10.1002/cnm.2991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/16/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
7
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Arvindekar S, Pathak AS, Majila K, Viswanath S. Optimizing representations for integrative structural modeling using Bayesian model selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571227. [PMID: 38168172 PMCID: PMC10760022 DOI: 10.1101/2023.12.12.571227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Preprint 2
24
Xie S, Saba L, Jiang H, Bringas OR, Oghbaie M, Stefano LD, Sherman V, LaCava J. Multiparameter screen optimizes immunoprecipitation. Biotechniques 2024;76:145-152. [PMID: 38425263 PMCID: PMC11091867 DOI: 10.2144/btn-2023-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]  Open
research-article 1
25
Pasani S, Menon KS, Viswanath S. The molecular architecture of the desmosomal outer dense plaque by integrative structural modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.13.544884. [PMID: 37398295 PMCID: PMC10312763 DOI: 10.1101/2023.06.13.544884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Preprint 1
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