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For: Saltzberg DJ, Broughton HB, Pellarin R, Chalmers MJ, Espada A, Dodge JA, Pascal BD, Griffin PR, Humblet C, Sali A. A Residue-Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen-Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions. J Phys Chem B 2016;121:3493-3501. [PMID: 27807976 DOI: 10.1021/acs.jpcb.6b09358] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Number Cited by Other Article(s)
1
Mann MD, Wang M, Ferreon JC, Tsoi PS, Suess MP, Jain A, Malovannaya A, Alvarez RV, Pascal BD, Kumar R, Edwards DP, Griffin PR. Structural proteomics defines a sequential priming mechanism for the progesterone receptor. Nat Commun 2025;16:4403. [PMID: 40355435 PMCID: PMC12069617 DOI: 10.1038/s41467-025-59458-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Accepted: 04/24/2025] [Indexed: 05/14/2025]  Open
2
Latham AP, Rožič M, Webb BM, Sali A. Tutorial on integrative spatiotemporal modeling by integrative modeling platform. Protein Sci 2025;34:e70107. [PMID: 40130765 PMCID: PMC11934212 DOI: 10.1002/pro.70107] [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: 12/05/2024] [Revised: 02/26/2025] [Accepted: 03/09/2025] [Indexed: 03/26/2025]
3
McLaughlin NK, Rincon Pabon JP, Gies S, Dastvan R, Gross ML. Kingfisher: An open-sourced web-based platform for the analysis of hydrogen exchange mass spectrometry data. Protein Sci 2025;34:e70096. [PMID: 40099873 PMCID: PMC11915630 DOI: 10.1002/pro.70096] [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: 09/12/2024] [Revised: 01/25/2025] [Accepted: 02/21/2025] [Indexed: 03/20/2025]
4
Stofella M, Grimaldi A, Smit JH, Claesen J, Paci E, Sobott F. Computational Tools for Hydrogen-Deuterium Exchange Mass Spectrometry Data Analysis. Chem Rev 2024;124:12242-12263. [PMID: 39481095 PMCID: PMC11565574 DOI: 10.1021/acs.chemrev.4c00438] [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: 06/10/2024] [Revised: 10/16/2024] [Accepted: 10/21/2024] [Indexed: 11/02/2024]
5
Turzo SMBA, Seffernick JT, Lyskov S, Lindert S. Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver. Brief Bioinform 2023;24:bbad308. [PMID: 37609950 PMCID: PMC10516336 DOI: 10.1093/bib/bbad308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/03/2023] [Accepted: 08/08/2023] [Indexed: 08/24/2023]  Open
6
Crook OM, Gittens N, Chung CW, Deane CM. A Functional Bayesian Model for Hydrogen-Deuterium Exchange Mass Spectrometry. J Proteome Res 2023;22:2959-2972. [PMID: 37582225 PMCID: PMC10476270 DOI: 10.1021/acs.jproteome.3c00297] [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: 05/15/2023] [Indexed: 08/17/2023]
7
Fundamentals of HDX-MS. Essays Biochem 2022;67:301-314. [PMID: 36251047 PMCID: PMC10070489 DOI: 10.1042/ebc20220111] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
8
Turzo SMBA, Seffernick JT, Rolland AD, Donor MT, Heinze S, Prell JS, Wysocki VH, Lindert S. Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction. Nat Commun 2022;13:4377. [PMID: 35902583 PMCID: PMC9334640 DOI: 10.1038/s41467-022-32075-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 07/14/2022] [Indexed: 11/09/2022]  Open
9
Tran MH, Schoeder CT, Schey KL, Meiler J. Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook. Front Immunol 2022;13:859964. [PMID: 35720345 PMCID: PMC9204306 DOI: 10.3389/fimmu.2022.859964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022]  Open
10
Yandrofski K, Mouchahoir T, De Leoz ML, Duewer D, Hudgens JW, Anderson KW, Arbogast L, Delaglio F, Brinson RG, Marino JP, Phinney K, Tarlov M, Schiel JE. Interlaboratory Studies Using the NISTmAb to Advance Biopharmaceutical Structural Analytics. Front Mol Biosci 2022;9:876780. [PMID: 35601836 PMCID: PMC9117750 DOI: 10.3389/fmolb.2022.876780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/21/2022] [Indexed: 01/18/2023]  Open
11
Stofella M, Skinner SP, Sobott F, Houwing-Duistermaat J, Paci E. High-Resolution Hydrogen-Deuterium Protection Factors from Sparse Mass Spectrometry Data Validated by Nuclear Magnetic Resonance Measurements. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022;33:813-822. [PMID: 35385652 PMCID: PMC9074100 DOI: 10.1021/jasms.2c00005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
12
Advances in Mass Spectrometry-based Epitope Mapping of Protein Therapeutics. J Pharm Biomed Anal 2022;215:114754. [DOI: 10.1016/j.jpba.2022.114754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/16/2022] [Accepted: 04/03/2022] [Indexed: 11/21/2022]
13
Crook OM, Chung CW, Deane CM. Challenges and Opportunities for Bayesian Statistics in Proteomics. J Proteome Res 2022;21:849-864. [PMID: 35258980 PMCID: PMC8982455 DOI: 10.1021/acs.jproteome.1c00859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Indexed: 12/27/2022]
14
Devaurs D, Antunes DA, Borysik AJ. Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022;33:215-237. [PMID: 35077179 DOI: 10.1021/jasms.1c00328] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
15
Salmas RE, Borysik AJ. Exploiting the Propagation of Constrained Variables for Enhanced HDX-MS Data Optimization. Anal Chem 2021;93:16417-16424. [PMID: 34860510 DOI: 10.1021/acs.analchem.1c03082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
16
Graziadei A, Rappsilber J. Leveraging crosslinking mass spectrometry in structural and cell biology. Structure 2021;30:37-54. [PMID: 34895473 DOI: 10.1016/j.str.2021.11.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/11/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022]
17
Hamuro Y. Quantitative Hydrogen/Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021;32:2711-2727. [PMID: 34749499 DOI: 10.1021/jasms.1c00216] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
18
Smit JH, Krishnamurthy S, Srinivasu BY, Parakra R, Karamanou S, Economou A. Probing Universal Protein Dynamics Using Hydrogen-Deuterium Exchange Mass Spectrometry-Derived Residue-Level Gibbs Free Energy. Anal Chem 2021;93:12840-12847. [PMID: 34523340 DOI: 10.1021/acs.analchem.1c02155] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
19
James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021;122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
20
Ziemianowicz DS, Saltzberg D, Pells T, Crowder DA, Schräder C, Hepburn M, Sali A, Schriemer DC. IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics. Mol Cell Proteomics 2021;20:100139. [PMID: 34418567 PMCID: PMC8452774 DOI: 10.1016/j.mcpro.2021.100139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 07/27/2021] [Accepted: 08/11/2021] [Indexed: 11/01/2022]  Open
21
Salmas RE, Borysik AJ. Characterization and Management of Noise in HDX-MS Data Modeling. Anal Chem 2021;93:7323-7331. [PMID: 33961396 DOI: 10.1021/acs.analchem.1c00894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
22
Jin N, Matter WF, Michael LF, Qian Y, Gheyi T, Cano L, Perez C, Lafuente C, Broughton HB, Espada A. The Angiopoietin-Like Protein 3 and 8 Complex Interacts with Lipoprotein Lipase and Induces LPL Cleavage. ACS Chem Biol 2021;16:457-462. [PMID: 33656326 DOI: 10.1021/acschembio.0c00954] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
23
Raval S, Sarpe V, Hepburn M, Crowder DA, Zhang T, Viner R, Schriemer DC. Improving Spectral Validation Rates in Hydrogen-Deuterium Exchange Data Analysis. Anal Chem 2021;93:4246-4254. [PMID: 33592142 DOI: 10.1021/acs.analchem.0c05045] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
24
HDXmodeller: an online webserver for high-resolution HDX-MS with auto-validation. Commun Biol 2021;4:199. [PMID: 33589746 PMCID: PMC7884430 DOI: 10.1038/s42003-021-01709-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022]  Open
25
Seffernick JT, Lindert S. Hybrid methods for combined experimental and computational determination of protein structure. J Chem Phys 2020;153:240901. [PMID: 33380110 PMCID: PMC7773420 DOI: 10.1063/5.0026025] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/10/2020] [Indexed: 02/04/2023]  Open
26
Gao S, Thompson EJ, Barrow SL, Zhang W, Iavarone AT, Klinman JP. Hydrogen-Deuterium Exchange within Adenosine Deaminase, a TIM Barrel Hydrolase, Identifies Networks for Thermal Activation of Catalysis. J Am Chem Soc 2020;142:19936-19949. [PMID: 33181018 DOI: 10.1021/jacs.0c07866] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
27
Engen JR, Botzanowski T, Peterle D, Georgescauld F, Wales TE. Developments in Hydrogen/Deuterium Exchange Mass Spectrometry. Anal Chem 2020;93:567-582. [DOI: 10.1021/acs.analchem.0c04281] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
28
Chang A, Ting JP, Espada A, Broughton H, Molina-Martin M, Afshar S. A novel phage display vector for selection of target-specific peptides. Protein Eng Des Sel 2020;33:5917485. [PMID: 33009572 DOI: 10.1093/protein/gzaa023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 11/14/2022]  Open
29
Pandya P, Sayers RO, Ting JP, Morshedian S, Torres C, Cudal JS, Zhang K, Fitchett JR, Zhang Q, Zhang FF, Wang J, Durbin JD, Carrillo JJ, Espada A, Broughton H, Qian Y, Afshar S. Integration of phage and yeast display platforms: A reliable and cost effective approach for binning of peptides as displayed on-phage. PLoS One 2020;15:e0233961. [PMID: 32479512 PMCID: PMC7263589 DOI: 10.1371/journal.pone.0233961] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 05/16/2020] [Indexed: 12/11/2022]  Open
30
Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020;120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
31
Wollenberg DTW, Pengelley S, Mouritsen JC, Suckau D, Jørgensen CI, Jørgensen TJD. Avoiding H/D Scrambling with Minimal Ion Transmission Loss for HDX-MS/MS-ETD Analysis on a High-Resolution Q-TOF Mass Spectrometer. Anal Chem 2020;92:7453-7461. [PMID: 32427467 DOI: 10.1021/acs.analchem.9b05208] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
32
Bradshaw RT, Marinelli F, Faraldo-Gómez JD, Forrest LR. Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles. Biophys J 2020;118:1649-1664. [PMID: 32105651 PMCID: PMC7136279 DOI: 10.1016/j.bpj.2020.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 01/12/2023]  Open
33
Zheng J, Strutzenberg T, Pascal BD, Griffin PR. Protein dynamics and conformational changes explored by hydrogen/deuterium exchange mass spectrometry. Curr Opin Struct Biol 2019;58:305-313. [DOI: 10.1016/j.sbi.2019.06.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 06/15/2019] [Accepted: 06/25/2019] [Indexed: 12/31/2022]
34
Saltzberg DJ, Hepburn M, Pilla KB, Schriemer DC, Lees-Miller SP, Blundell TL, Sali A. SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019;147:92-102. [PMID: 31570166 DOI: 10.1016/j.pbiomolbio.2019.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/09/2019] [Accepted: 09/10/2019] [Indexed: 01/19/2023]
35
Babić D, Kazazić S, Smith DM. Resolution of protein hydrogen/deuterium exchange by fitting amide exchange probabilities to the peptide isotopic envelopes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019;33:1248-1257. [PMID: 31034666 DOI: 10.1002/rcm.8460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/13/2019] [Accepted: 04/10/2019] [Indexed: 05/11/2023]
36
Vallat B, Webb B, Westbrook J, Sali A, Berman HM. Archiving and disseminating integrative structure models. JOURNAL OF BIOMOLECULAR NMR 2019;73:385-398. [PMID: 31278630 PMCID: PMC6692293 DOI: 10.1007/s10858-019-00264-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/25/2019] [Indexed: 05/04/2023]
37
Estimating Constraints for Protection Factors from HDX-MS Data. Biophys J 2019;116:1194-1203. [PMID: 30885379 PMCID: PMC6451051 DOI: 10.1016/j.bpj.2019.02.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/21/2019] [Accepted: 02/26/2019] [Indexed: 11/22/2022]  Open
38
Benhaim M, Lee KK, Guttman M. Tracking Higher Order Protein Structure by Hydrogen-Deuterium Exchange Mass Spectrometry. Protein Pept Lett 2019;26:16-26. [PMID: 30543159 PMCID: PMC6386625 DOI: 10.2174/0929866526666181212165037] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/30/2018] [Accepted: 11/17/2018] [Indexed: 12/27/2022]
39
Sayago C, Gonzalez Valcarcel IC, Qian Y, Lee J, Alsina-Fernandez J, Fite NC, Carrillo JJ, Zhang FF, Chalmers MJ, Dodge JA, Broughton H, Espada A. Deciphering Binding Interactions of IL-23R with HDX-MS: Mapping Protein and Macrocyclic Dodecapeptide Ligands. ACS Med Chem Lett 2018;9:912-916. [PMID: 30258540 DOI: 10.1021/acsmedchemlett.8b00255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/01/2018] [Indexed: 11/29/2022]  Open
40
MS methods to study macromolecule-ligand interaction: Applications in drug discovery. Methods 2018;144:152-174. [PMID: 29890284 DOI: 10.1016/j.ymeth.2018.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 12/12/2022]  Open
41
Aprahamian ML, Chea EE, Jones LM, Lindert S. Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data. Anal Chem 2018;90:7721-7729. [PMID: 29874044 DOI: 10.1021/acs.analchem.8b01624] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
42
Politis A, Schmidt C. Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling. J Proteomics 2018;175:34-41. [DOI: 10.1016/j.jprot.2017.04.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/13/2017] [Accepted: 04/18/2017] [Indexed: 01/14/2023]
43
Ting JP, Tung F, Antonysamy S, Wasserman S, Jones SB, Zhang FF, Espada A, Broughton H, Chalmers MJ, Woodman ME, Bina HA, Dodge JA, Benach J, Zhang A, Groshong C, Manglicmot D, Russell M, Afshar S. Utilization of peptide phage display to investigate hotspots on IL-17A and what it means for drug discovery. PLoS One 2018;13:e0190850. [PMID: 29329326 PMCID: PMC5766103 DOI: 10.1371/journal.pone.0190850] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022]  Open
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Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures. Biophys J 2018;113:2344-2353. [PMID: 29211988 DOI: 10.1016/j.bpj.2017.10.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/22/2017] [Accepted: 10/02/2017] [Indexed: 12/22/2022]  Open
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Webb B, Viswanath S, Bonomi M, Pellarin R, Greenberg CH, Saltzberg D, Sali A. Integrative structure modeling with the Integrative Modeling Platform. Protein Sci 2017;27:245-258. [PMID: 28960548 DOI: 10.1002/pro.3311] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/23/2017] [Accepted: 09/25/2017] [Indexed: 11/06/2022]
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Gessner C, Steinchen W, Bédard S, J Skinner J, Woods VL, Walsh TJ, Bange G, Pantazatos DP. Computational method allowing Hydrogen-Deuterium Exchange Mass Spectrometry at single amide Resolution. Sci Rep 2017. [PMID: 28630467 PMCID: PMC5476592 DOI: 10.1038/s41598-017-03922-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
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