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For: Ziegler SJ, Mallinson SJ, St. John PC, Bomble YJ. Advances in integrative structural biology: Towards understanding protein complexes in their cellular context. Comput Struct Biotechnol J 2020;19:214-225. [PMID: 33425253 PMCID: PMC7772369 DOI: 10.1016/j.csbj.2020.11.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 01/26/2023]  Open
Number Cited by Other Article(s)
1
Laurent B, Lanrezac A, Santuz H, Ferey N, Delalande O, Baaden M. BioSpring: An elastic network framework for interactive exploration of macromolecular mechanics. Protein Sci 2025;34:e70130. [PMID: 40249023 PMCID: PMC12006919 DOI: 10.1002/pro.70130] [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: 10/31/2024] [Revised: 03/07/2025] [Accepted: 04/06/2025] [Indexed: 04/19/2025]
2
Iram F, Aiman A, Vijh D, Shahid M, Choudhir G, Khan T, Alam D, Hassan MI, Islam A. Unraveling the catalase dynamics: Biophysical and computational insights into co-solutes driven stabilization under extreme pH conditions. Int J Biol Macromol 2025;301:140467. [PMID: 39884626 DOI: 10.1016/j.ijbiomac.2025.140467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 01/24/2025] [Accepted: 01/27/2025] [Indexed: 02/01/2025]
3
Tran MH, Martina CE, Moretti R, Nagel M, Schey KL, Meiler J. RosettaHDX: Predicting antibody-antigen interaction from hydrogen-deuterium exchange mass spectrometry data. J Struct Biol 2025;217:108166. [PMID: 39765317 PMCID: PMC12010952 DOI: 10.1016/j.jsb.2025.108166] [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: 10/01/2024] [Revised: 12/06/2024] [Accepted: 01/04/2025] [Indexed: 01/20/2025]
4
Rosignoli S, Pacelli M, Manganiello F, Paiardini A. An outlook on structural biology after AlphaFold: tools, limits and perspectives. FEBS Open Bio 2025;15:202-222. [PMID: 39313455 PMCID: PMC11788754 DOI: 10.1002/2211-5463.13902] [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: 03/13/2024] [Revised: 08/19/2024] [Accepted: 09/13/2024] [Indexed: 09/25/2024]  Open
5
Cui Z, Liu X, E T, Lin H, Wang D, Liu Y, Ruan X, Wang P, Liu L, Xue Y. Effect of SNORD113-3/ADAR2 on glycolipid metabolism in glioblastoma via A-to-I editing of PHKA2. Cell Mol Biol Lett 2025;30:5. [PMID: 39794701 PMCID: PMC11724473 DOI: 10.1186/s11658-024-00680-9] [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: 05/15/2024] [Accepted: 12/17/2024] [Indexed: 01/13/2025]  Open
6
le Maire A, Bourguet W. What Structural Biology Tells Us About the Mode of Action and Detection of Toxicants. Annu Rev Pharmacol Toxicol 2025;65:529-546. [PMID: 39107041 DOI: 10.1146/annurev-pharmtox-061724-080642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2024]
7
Xue Z, Sun C, Zheng W, Lv J, Liu X. TargetSA: adaptive simulated annealing for target-specific drug design. Bioinformatics 2024;41:btae730. [PMID: 39656791 PMCID: PMC12013812 DOI: 10.1093/bioinformatics/btae730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 10/28/2024] [Accepted: 12/02/2024] [Indexed: 12/17/2024]  Open
8
Zhao Y, Singh K, Chowdary Karuturi R, Hefny AA, Shakeri A, Beazely MA, Rao PPN. Benzofuran and Benzo[b]thiophene-2-Carboxamide Derivatives as Modulators of Amyloid Beta (Aβ42) Aggregation. ChemMedChem 2024;19:e202400198. [PMID: 39083696 PMCID: PMC11581421 DOI: 10.1002/cmdc.202400198] [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: 03/15/2024] [Revised: 07/25/2024] [Accepted: 07/31/2024] [Indexed: 08/02/2024]
9
Pellequer JL. Perspectives Toward an Integrative Structural Biology Pipeline With Atomic Force Microscopy Topographic Images. J Mol Recognit 2024;37:e3102. [PMID: 39329418 DOI: 10.1002/jmr.3102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/21/2024] [Accepted: 09/03/2024] [Indexed: 09/28/2024]
10
Wang CR, McFarlane LO, Pukala TL. Exploring snake venoms beyond the primary sequence: From proteoforms to protein-protein interactions. Toxicon 2024;247:107841. [PMID: 38950738 DOI: 10.1016/j.toxicon.2024.107841] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
11
Turkoglu B, Mansuroglu B. Investigating the Effects of Chelidonic Acid on Oxidative Stress-Induced Premature Cellular Senescence in Human Skin Fibroblast Cells. Life (Basel) 2024;14:1070. [PMID: 39337855 PMCID: PMC11433492 DOI: 10.3390/life14091070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/18/2024] [Accepted: 08/20/2024] [Indexed: 09/30/2024]  Open
12
Chihomvu P, Ganesan A, Gibbons S, Woollard K, Hayes MA. Phytochemicals in Drug Discovery-A Confluence of Tradition and Innovation. Int J Mol Sci 2024;25:8792. [PMID: 39201478 PMCID: PMC11354359 DOI: 10.3390/ijms25168792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 09/02/2024]  Open
13
Durbin KR, Robey MT, Voong LN, Fellers RT, Lutomski CA, El-Baba TJ, Robinson CV, Kelleher NL. ProSight Native: Defining Protein Complex Composition from Native Top-Down Mass Spectrometry Data. J Proteome Res 2023;22:2660-2668. [PMID: 37436406 PMCID: PMC10407923 DOI: 10.1021/acs.jproteome.3c00171] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Indexed: 07/13/2023]
14
Mondal A, Lenz S, MacCallum JL, Perez A. Hybrid computational methods combining experimental information with molecular dynamics. Curr Opin Struct Biol 2023;81:102609. [PMID: 37224642 DOI: 10.1016/j.sbi.2023.102609] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/12/2023] [Accepted: 04/23/2023] [Indexed: 05/26/2023]
15
Hvorecny KL, Kollman JM. Greater than the sum of parts: Mechanisms of metabolic regulation by enzyme filaments. Curr Opin Struct Biol 2023;79:102530. [PMID: 36709625 PMCID: PMC10023394 DOI: 10.1016/j.sbi.2023.102530] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/28/2022] [Accepted: 12/19/2022] [Indexed: 01/28/2023]
16
Santorelli L, Caterino M, Costanzo M. Dynamic Interactomics by Cross-Linking Mass Spectrometry: Mapping the Daily Cell Life in Postgenomic Era. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022;26:633-649. [PMID: 36445175 DOI: 10.1089/omi.2022.0137] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
17
Huang W, Sun YM, Pan Q, Fang K, Chen XT, Zeng ZC, Chen TQ, Zhu SX, Huang LB, Luo XQ, Wang WT, Chen YQ. The snoRNA-like lncRNA LNC-SNO49AB drives leukemia by activating the RNA-editing enzyme ADAR1. Cell Discov 2022;8:117. [PMID: 36316318 PMCID: PMC9622897 DOI: 10.1038/s41421-022-00460-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 08/18/2022] [Indexed: 01/24/2023]  Open
18
Vakser IA, Grudinin S, Jenkins NW, Kundrotas PJ, Deeds EJ. Docking-based long timescale simulation of cell-size protein systems at atomic resolution. Proc Natl Acad Sci U S A 2022;119:e2210249119. [PMID: 36191203 PMCID: PMC9565162 DOI: 10.1073/pnas.2210249119] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/02/2022] [Indexed: 01/03/2023]  Open
19
Hofmann L, Ruthstein S. EPR Spectroscopy Provides New Insights into Complex Biological Reaction Mechanisms. J Phys Chem B 2022;126:7486-7494. [PMID: 36137278 PMCID: PMC9549461 DOI: 10.1021/acs.jpcb.2c05235] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
20
Blackburn MR, Minkoff BB, Sussman MR. Mass spectrometry-based technologies for probing the 3D world of plant proteins. PLANT PHYSIOLOGY 2022;189:12-22. [PMID: 35139210 PMCID: PMC9070838 DOI: 10.1093/plphys/kiac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/30/2021] [Indexed: 05/03/2023]
21
Molza AE, Westermaier Y, Moutte M, Ducrot P, Danilowicz C, Godoy-Carter V, Prentiss M, Robert CH, Baaden M, Prévost  C. Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Front Mol Biosci 2022;9:826136. [PMID: 35480882 PMCID: PMC9035671 DOI: 10.3389/fmolb.2022.826136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/21/2022] [Indexed: 01/25/2023]  Open
22
Yunoki Y, Matsumoto A, Morishima K, Martel A, Porcar L, Sato N, Yogo R, Tominaga T, Inoue R, Yagi-Utsumi M, Okuda A, Shimizu M, Urade R, Terauchi K, Kono H, Yagi H, Kato K, Sugiyama M. Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach. Commun Biol 2022;5:184. [PMID: 35273347 PMCID: PMC8913699 DOI: 10.1038/s42003-022-03143-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/08/2022] [Indexed: 12/24/2022]  Open
23
Ni D, Liu Y, Kong R, Yu Z, Lu S, Zhang J. Computational elucidation of allosteric communication in proteins for allosteric drug design. Drug Discov Today 2022;27:2226-2234. [DOI: 10.1016/j.drudis.2022.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/22/2022] [Accepted: 03/17/2022] [Indexed: 02/07/2023]
24
Wood DM, Dobson RC, Horne CR. Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation. Biochem Soc Trans 2021;49:2711-2726. [PMID: 34854920 PMCID: PMC8786299 DOI: 10.1042/bst20210674] [Citation(s) in RCA: 4] [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: 10/01/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 11/17/2022]
25
Piersimoni L, Kastritis PL, Arlt C, Sinz A. Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein-Protein Interactions─A Method for All Seasons. Chem Rev 2021;122:7500-7531. [PMID: 34797068 DOI: 10.1021/acs.chemrev.1c00786] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
26
Lyonnais S, Sadiq SK, Lorca-Oró C, Dufau L, Nieto-Marquez S, Escribà T, Gabrielli N, Tan X, Ouizougun-Oubari M, Okoronkwo J, Reboud-Ravaux M, Gatell JM, Marquet R, Paillart JC, Meyerhans A, Tisné C, Gorelick RJ, Mirambeau G. The HIV-1 Nucleocapsid Regulates Its Own Condensation by Phase-Separated Activity-Enhancing Sequestration of the Viral Protease during Maturation. Viruses 2021;13:v13112312. [PMID: 34835118 PMCID: PMC8625067 DOI: 10.3390/v13112312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023]  Open
27
Schaeffer RD, Kinch LN, Pei J, Medvedev KE, Grishin NV. Completeness and Consistency in Structural Domain Classifications. ACS OMEGA 2021;6:15698-15707. [PMID: 34179613 PMCID: PMC8223206 DOI: 10.1021/acsomega.1c00950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/25/2021] [Indexed: 06/13/2023]
28
Gardner A, Autin L, Fuentes D, Maritan M, Barad BA, Medina M, Olson AJ, Grotjahn DA, Goodsell DS. CellPAINT: Turnkey Illustration of Molecular Cell Biology. FRONTIERS IN BIOINFORMATICS 2021;1:660936. [PMID: 34790910 PMCID: PMC8594902 DOI: 10.3389/fbinf.2021.660936] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/08/2021] [Indexed: 01/01/2023]  Open
29
Sali A. From integrative structural biology to cell biology. J Biol Chem 2021;296:100743. [PMID: 33957123 PMCID: PMC8203844 DOI: 10.1016/j.jbc.2021.100743] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/09/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022]  Open
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