xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints

D³ Data-Driven Documents

Bostock, M., Ogievetsky, V., & Heer, J. (2011) · IEEE Transactions on Visualization and Computer Graphics · doi:10.1109/tvcg.2011.185 · Cited by 3,165

ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information

Glaser, F., Pupko, T., Paz, I., Bell, R. E., Shental-Bechor, D., Martz, E., & Ben‐Tal, N. (2002) · Bioinformatics · doi:10.1093/bioinformatics/19.1.163 · Cited by 1,237

Chemical cross‐linking and mass spectrometry to map three‐dimensional protein structures and protein–protein interactions

Sinz, A. (2006) · Mass Spectrometry Reviews · doi:10.1002/mas.20082 · Cited by 648

Determining the architectures of macromolecular assemblies

Alber, F., Dokudovskaya, S., Veenhoff, L. M., Zhang, W., Kipper, J., Devos, D. P., Suprapto, A., Karni-Schmidt, O., Williams, R., Chait, B. T., et al. (2007) · Nature · doi:10.1038/nature06404 · Cited by 525

Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics

Leitner, A., Walzthoeni, T., Kahraman, A., Herzog, F., Rinner, O., Beck, M., & Aebersold, R. H. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r000001-mcp201 · Cited by 468

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

Lasker, K., Förster, F. G., Bohn, S., Walzthoeni, T., Villa, E., Unverdorben, P., Beck, F., Aebersold, R. H., Šali, A., & Baumeister, W. P. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120559109 · Cited by 442

Using MCL to Extract Clusters from Networks

van Dongen, S., & Abreu‐Goodger, C. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-361-5_15 · Cited by 432

Development of a Novel Cross-linking Strategy for Fast and Accurate Identification of Cross-linked Peptides of Protein Complexes

Kao, A., Chiu, C., Vellucci, D., Yang, Y., Patel, V. R., Guan, S., Randall, A. Z., Baldi, P., Rychnovsky, S. D., & Huang, L. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.002212 · Cited by 405

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

Herzog, F., Kahraman, A., Boehringer, D., Mak, R., Bracher, A., Walzthoeni, T., Leitner, A., Beck, M., Hartl, F. U., Ban, N., et al. (2012) · Science · doi:10.1126/science.1221483 · Cited by 372

Integrated Structural Analysis of the Human Nuclear Pore Complex Scaffold

Bui, K. H., von Appen, A., DiGuilio, A. L., Ori‬‬, A., Sparks, L., Mackmull, M., Bock, T., Hagen, W. J. H., Andrés‐Pons, A., Glavy, J. S., et al. (2013) · Cell · doi:10.1016/j.cell.2013.10.055 · Cited by 351

Structure of the human MHC-I peptide-loading complex

Blees, A., Januliene, D., Hofmann, T., Koller, N., Schmidt, C., Trowitzsch, S., Moeller, A., & Tampé, R. (2017) · Nature · doi:10.1038/nature24627 · Cited by 372

Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology

O’Reilly, F. J., & Rappsilber, J. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0147-0 · Cited by 366

Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines

Leitner, A., Faini, M., Stengel, F., & Aebersold, R. H. (2015) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2015.10.008 · Cited by 368

Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology

Yu, C., & Huang, L. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b04431 · Cited by 344

Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein–Protein Interactions─A Method for All Seasons

Piersimoni, L., Kastritis, P. L., Arlt, C., & Sinz, A. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00786 · Cited by 327

Inert and seed-competent tau monomers suggest structural origins of aggregation

Mirbaha, H., Chen, D., Morazova, O. A., Ruff, K. M., Sharma, A. M., Liu, X., Goodarzi, M., Pappu, R. V., Colby, D. W., Mirzaei, H., et al. (2018) · eLife · doi:10.7554/elife.36584 · Cited by 225

Structural insights into preinitiation complex assembly on core promoters

Chen, X., Qi, Y., Wu, Z., Wang, X., Li, J., Zhao, D., Hou, H., Li, Y., Yu, Z., Liu, W., et al. (2021) · Science · doi:10.1126/science.aba8490 · Cited by 185

Structures of the human Mediator and Mediator-bound preinitiation complex

Chen, X., Yin, X., Li, J., Wu, Z., Qi, Y., Wang, X., Liu, W., & Xu, Y. (2021) · Science · doi:10.1126/science.abg0635 · Cited by 186

A unified mechanism for intron and exon definition and back-splicing

Li, X., Liu, S., Zhang, L., Issaian, A., Hill, R. C., Espinosa, S., Shi, S., Cui, Y., Kappel, K., Das, R., et al. (2019) · Nature · doi:10.1038/s41586-019-1523-6 · Cited by 177

Human Condensin I and II Drive Extensive ATP-Dependent Compaction of Nucleosome-Bound DNA

Kong, M., Cutts, E., Pan, D., Beuron, F., Kaliyappan, T., Xue, C., Morris, E. P., Musacchio, A., Vannini, A., & Greene, E. C. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.04.026 · Cited by 162

Insights from biochemical reconstitution into the architecture of human kinetochores

Weir, J. R., Faesen, A. C., Klare, K., Petrović, A., Basilico, F., Fischböck, J., Pentakota, S., Keller, J., Pesenti, M. E., Pan, D., et al. (2016) · Nature · doi:10.1038/nature19333 · Cited by 156

ATG9A and ATG2A form a heteromeric complex essential for autophagosome formation

van Vliet, A. R., Chiduza, G. N., Maslen, S., Pye, V. E., Joshi, D., Tito, S. D., Jefferies, H. B. J., Christodoulou, E., Roustan, C., Punch, E. K., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.10.017 · Cited by 146

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

Wagner, F., Dienemann, C., Wang, H., Stützer, A., Tegunov, D., Urlaub, H., & Cramer, P. (2020) · Nature · doi:10.1038/s41586-020-2088-0 · Cited by 148

PyXlinkViewer : A flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system

Schiffrin, B., Radford, S. E., Brockwell, D. J., & Calabrese, A. N. (2020) · Protein Science · doi:10.1002/pro.3902 · Cited by 136

Mapping of the plant SnRK1 kinase signalling network reveals a key regulatory role for the class II T6P synthase-like proteins

Leene, J. V., Eeckhout, D., Gadeyne, A., Matthijs, C., Han, C., Winne, N. D., Persiau, G., Slijke, E. V. D., Persyn, F., Mertens, T., et al. (2022) · Nature Plants · doi:10.1038/s41477-022-01269-w · Cited by 136

Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome

Yan, K., Yang, J., Zhang, Z., McLaughlin, S. H., Chang, L., Fasci, D., Ehrenhofer‐Murray, A. E., Heck, A. J. R., & Barford, D. (2019) · Nature · doi:10.1038/s41586-019-1609-1 · Cited by 137

A RECK-WNT7 Receptor-Ligand Interaction Enables Isoform-Specific Regulation of Wnt Bioavailability

Vallon, M., Yuki, K., Nguyen, T. D., Chang, J., Yuan, J., Siepe, D. H., Miao, Y., Essler, M., Noda, M., García, K. C., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.09.045 · Cited by 124

xiView: A common platform for the downstream analysis of Crosslinking Mass Spectrometry dataPreprint

Graham, M., Combe, C., Kolbowski, L., & Rappsilber, J. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/561829 · Cited by 97

The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA

Deep, A., Gu, Y., Gao, Y.-Q., Ego, K. M., Herzik, M. A., Zhou, H., & Corbett, K. D. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.09.008 · Cited by 106

xiVIEW: Visualisation of Crosslinking Mass Spectrometry Data

Combe, C., Graham, M., Kolbowski, L., Fischer, L., & Rappsilber, J. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168656 · Cited by 103

Critical Role of the UBL Domain in Stimulating the E3 Ubiquitin Ligase Activity of UHRF1 toward Chromatin

Foster, B. M., Stolz, P., Mulholland, C. B., Montoya, A., Kramer, H., Bultmann, S., & Bartke, T. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.09.028 · Cited by 99

The COMA complex interacts with Cse4 and positions Sli15/Ipl1 at the budding yeast inner kinetochore

Fischböck, J., Singh, S., Potočnjak, M., Hagemann, G., Solis‐Mezarino, V., Woike, S., Ghodgaonkar-Steger, M., Weissmann, F., Gallego, L. D., Rojas, J., et al. (2019) · eLife · doi:10.7554/elife.42879 · Cited by 93

Combining cryo-electron microscopy (cryo-EM) and cross-linking mass spectrometry (CX-MS) for structural elucidation of large protein assemblies

Schmidt, C., & Urlaub, H. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.10.005 · Cited by 91

CDC20 assists its catalytic incorporation in the mitotic checkpoint complex

Piano, V., Alex, A., Stege, P., Maffini, S., Stoppiello, G. A., Veld, P. J. H. I. ’., Vetter, I. R., & Musacchio, A. (2020) · Science · doi:10.1126/science.abc1152 · Cited by 88

Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein–Protein Interaction Networks in Vivo

Matzinger, M., & Mechtler, K. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00583 · Cited by 84

Cross-linking/mass spectrometry to get a closer view on protein interaction networks

Iacobucci, C., Götze, M., & Sinz, A. (2019) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2019.12.009 · Cited by 82

Mapping the multiscale structure of biological systems

Schaffer, L. V., & Ideker, T. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.012 · Cited by 75

Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data

Orbán-Németh, Z., Beveridge, R., Hollenstein, D. M., Rampler, E., Stranzl, T., Hudecz, O., Doblmann, J., Schlögelhofer, P., & Mechtler, K. (2018) · Nature Protocols · doi:10.1038/nprot.2017.146 · Cited by 72

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data

Riffle, M. E., Jaschob, D., Zelter, A., & Davis, T. N. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00274 · Cited by 65

Integrated Workflow for Structural Proteomics Studies Based on Cross-Linking/Mass Spectrometry with an MS/MS Cleavable Cross-Linker

Arlt, C., Götze, M., Ihling, C. H., Hage, C., Schäfer, M., & Sinz, A. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04853 · Cited by 69

The Nucleosome Remodeling and Deacetylase Complex Has an Asymmetric, Dynamic, and Modular Architecture

Low, J. K. K., Silva, A. P. G., Tabar, M. S., Torrado, M., Webb, S. R., Parker, B. L., Sana, M., Smits, C., Schmidberger, J. W., Brillault, L., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108450 · Cited by 65

CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing

Li, X., Liu, S., Jiang, J., Zhang, L., Espinosa, S., Hill, R. C., Hansen, K. C., Zhou, Z. H., & Zhao, R. (2017) · Nature Communications · doi:10.1038/s41467-017-01241-9 · Cited by 66

Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome

Faull, S. V., Lau, A. M., Martens, C., Ahdash, Z., Hansen, K., Yébenes, H., Schmidt, C., Beuron, F., Cronin, N., Morris, E. P., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11772-y · Cited by 66

Cryo-EM structure of the Mre11-Rad50-Nbs1 complex reveals the molecular mechanism of scaffolding functions

Rotheneder, M., Stakyte, K., van de Logt, E., Bartho, J. D., Lammens, K., Fan, Y., Alt, A., Keßler, B., Jung, C., Roos, W. P., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.12.003 · Cited by 65

Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

Sundaramoorthy, R., Hughes, A. L., Singh, V., Wiechens, N., Ryan, D., Mkami, H. E., Petoukhov, M. V., Svergun, D. I., Treutlein, B., Quack, S., et al. (2017) · eLife · doi:10.7554/elife.22510 · Cited by 62

The linear ubiquitin chain assembly complex (LUBAC) generates heterotypic ubiquitin chains

Carvajal, A. R., Grishkovskaya, I., Diaz, C. G., Vogel, A., Sonn-Segev, A., Kushwah, M. S., Schodl, K., Deszcz, L., Orbán-Németh, Z., Sakamoto, S., et al. (2021) · eLife · doi:10.7554/elife.60660 · Cited by 58

A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria

Linden, A., Deckers, M., Parfentev, I., Pflanz, R., Homberg, B., Neumann, P., Ficner, R., Rehling, P., & Urlaub, H. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra120.002028 · Cited by 58

Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry

Leitner, A., Bonvin, A. M. J. J., Borchers, C. H., Chalkley, R. J., Chamot‐Rooke, J., Combe, C., Cox, J., Dong, M., Fischer, L., Götze, M., et al. (2020) · Structure · doi:10.1016/j.str.2020.09.011 · Cited by 58

SLIRP stabilizes LRPPRC via an RRM–PPR protein interface

Spåhr, H., Rozanska, A. L., Li, X., Atanassov, I., Lightowlers, R. N., Chrzanowska‐Lightowlers, Z. M., Rackham, O., & Larsson, N. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw575 · Cited by 55

Cross-Linking/Mass Spectrometry Combined with Ion Mobility on a timsTOF Pro Instrument for Structural Proteomics

Ihling, C. H., Piersimoni, L., Kipping, M., & Sinz, A. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c01317 · Cited by 56

Structural basis for the disaggregase activity and regulation of Hsp104

Heuck, A., Schitter-Sollner, S., Suskiewicz, M. J., Kurzbauer, R., Kley, J., Schleiffer, A., Rombaut, P., Herzog, F., & Clausen, T. (2016) · eLife · doi:10.7554/elife.21516 · Cited by 53

Cross-linking mass spectrometry uncovers protein interactions and functional assemblies in synaptic vesicle membranes

Wittig, S., Ganzella, M., Barth, M., Kostmann, S., Riedel, D., Pérez-Lara, Á., Jahn, R., & Schmidt, C. (2021) · Nature Communications · doi:10.1038/s41467-021-21102-w · Cited by 59

Bin1 directly remodels actin dynamics through its BAR domain

Dräger, N. M., Nachman, E., Winterhoff, M., Brühmann, S., Shah, P., Katsinelos, T., Boulant, S., Teleman, A. A., Faix, J., & Jahn, T. R. (2017) · The EMBO Reports · doi:10.15252/embr.201744137 · Cited by 51

Nucleosome binding by the pioneer transcription factor OCT4

Echigoya, K., Koyama, M., Negishi, L., Takizawa, Y., Mizukami, Y., Shimabayashi, H., Kuroda, A., & Kurumizaka, H. (2020) · Scientific Reports · doi:10.1038/s41598-020-68850-1 · Cited by 47

Structure based biophysical characterization of the PROPPIN Atg18 shows Atg18 oligomerization upon membrane binding

Scacioc, A., Schmidt, C., Hofmann, T., Urlaub, H., Kühnel, K., & Pérez-Lara, Á. (2017) · Scientific Reports · doi:10.1038/s41598-017-14337-5 · Cited by 44

Molecular architecture of the endocytic TPLATE complex

Yperman, K., Wang, J., Eeckhout, D., Winkler, J., Vu, L. D., Vandorpe, M., Grones, P., Mylle, E., Kraus, M., Merceron, R., et al. (2021) · Science Advances · doi:10.1126/sciadv.abe7999 · Cited by 46

Simplified Protocol for Cross-linking Mass Spectrometry Using the MS-Cleavable Cross-linker DSBU with Efficient Cross-link Identification

Pan, D., Brockmeyer, A., Müller, F., Musacchio, A., & Bange, T. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b02593 · Cited by 45

Structural mechanism for the recognition and ubiquitination of a single nucleosome residue by Rad6–Bre1

Gallego, L. D., Ghodgaonkar-Steger, M., Polyansky, A. A., Schubert, T., Žagrović, B., Zheng, N., Clausen, T., Herzog, F., & Köhler, A. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1606863113 · Cited by 43

Molecular requirements for the inter-subunit interaction and kinetochore recruitment of SKAP and Astrin

Friese, A., Faesen, A. C., Veld, P. J. H. I. ’., Fischböck, J., Prumbaum, D., Petrović, A., Raunser, S., Herzog, F., & Musacchio, A. (2016) · Nature Communications · doi:10.1038/ncomms11407 · Cited by 40

Structure of a Tc holotoxin pore provides insights into the translocation mechanism

Roderer, D., Hofnagel, O., Benz, R., & Raunser, S. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1909821116 · Cited by 40

Structural basis of TRAPPIII‐mediated Rab1 activation

Joiner, A. M. N., Phillips, B. P., Yugandhar, K., Sanford, E. J., Smolka, M. B., Yu, H., Miller, E. A., & Fromme, J. C. (2021) · The EMBO Journal · doi:10.15252/embj.2020107607 · Cited by 38

Conformational transitions of the Spindly adaptor underlie its interaction with Dynein and Dynactin

d’Amico, E. A., Ud Din Ahmad, M., Cmentowski, V., Girbig, M., Müller, F., Wohlgemuth, S., Brockmeyer, A., Maffini, S., Janning, P., Vetter, I. R., et al. (2022) · Journal of Cell Biology · doi:10.1083/jcb.202206131 · Cited by 34

Novel mechanistic insights into the role of Mer2 as the keystone of meiotic DNA break formation

Rousová, D., Nivsarkar, V., Altmannová, V., Funk, S. K., Raina, V. B., Liedtke, D., Janning, P., Müller, F., Reichle, H., Vader, G., et al. (2021) · eLife · doi:10.7554/elife.72330 · Cited by 38

Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease

Gómez‐Serrano, M., Camafeita, E., Loureiro, M., & Peral, B. (2018) · Oxidative Medicine and Cellular Longevity · doi:10.1155/2018/1435934 · Cited by 38

Cross‐linked peptide identification: A computational forest of algorithms

Yılmaz, Ş., Shiferaw, G. A., Rayó, J., Economou, A., Martens, L., & Vandermarliere, E. (2018) · Mass Spectrometry Reviews · doi:10.1002/mas.21559 · Cited by 37

Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry: Implications for the overall hKGDHc structure

Nagy, B., Polak, M., Ozohanics, O., Zámbó, Z., Szabó, E., Hubert, Á., Jordan, F., Nováček, J., Ádám‐Vizi, V., & Ambrus, A. (2021) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2021.129889 · Cited by 33

Loquacious-PD facilitates Drosophila Dicer-2 cleavage through interactions with the helicase domain and dsRNA

Trettin, K., Sinha, N. K., Eckert, D. M., Apple, S. E., & Bass, B. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1707063114 · Cited by 33

Insights from the reconstitution of the divergent outer kinetochore of Drosophila melanogaster

Liu, Y., Petrović, A., Rombaut, P., Mosalaganti, S., Keller, J., Raunser, S., Herzog, F., & Musacchio, A. (2016) · Open Biology · doi:10.1098/rsob.150236 · Cited by 32

Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1

Osakabe, A., Takizawa, Y., Horikoshi, N., Hatazawa, S., Negishi, L., Sato, S., Berger, F., Kakutani, T., & Kurumizaka, H. (2024) · Nature Communications · doi:10.1038/s41467-024-49465-w · Cited by 30

A multipronged approach unravels unprecedented protein–protein interactions in the human 2-oxoglutarate dehydrogenase multienzyme complex

Zhou, J., Yang, L., Ozohanics, O., Zhang, X., Wang, J., Ambrus, A., Arjunan, P., Brukh, R., Nemeria, N. S., Furey, W. F., et al. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.005432 · Cited by 27

A Click‐Chemistry‐Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry

Stadlmeier, M., Runtsch, L. S., Streshnev, F., Wühr, M., & Carell, T. (2019) · ChemBioChem · doi:10.1002/cbic.201900611 · Cited by 28

Molecular architecture of the augmin complex

Gabel, C. A., Li, Z., DeMarco, A. G., Zhang, Z., Yang, J., Hall, M. C., Barford, D., & Chang, L. (2022) · Nature Communications · doi:10.1038/s41467-022-33227-7 · Cited by 28

Toward an Understanding of the Structural and Mechanistic Aspects of Protein-Protein Interactions in 2-Oxoacid Dehydrogenase Complexes

Nemeria, N. S., Zhang, X., Leandro, J., Zhou, J., Yang, L., Houten, S. M., & Jordan, F. (2021) · Life · doi:10.3390/life11050407 · Cited by 27

The augmin complex architecture reveals structural insights into microtubule branching

Župa, E., Würtz, M., Neuner, A., Hoffmann, T., Rettel, M., Böhler, A., Vermeulen, B. J. A., Eustermann, S., Schiebel, E., & Pfeffer, S. (2022) · Nature Communications · doi:10.1038/s41467-022-33228-6 · Cited by 26

Introduction of a bounded penalty function in contact‐assisted simulations of protein structures to omit false restraints

Lubecka, E. A., & Liwo, A. (2019) · Journal of Computational Chemistry · doi:10.1002/jcc.25847 · Cited by 23

XlinkCyNET: A Cytoscape Application for Visualization of Protein Interaction Networks Based on Cross-Linking Mass Spectrometry Identifications

Lima, D. B., Zhu, Y., & Liu, F. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00957 · Cited by 23

Transglutaminase 2 has higher affinity for relaxed than for stretched fibronectin fibers

Selcuk, K., Leitner, A., Braun, L., Blanc, F. L., Pacak, P., Pot, S. A., & Viola Vogel, B. (2023) · Matrix Biology · doi:10.1016/j.matbio.2023.12.006 · Cited by 21

Phospho‐regulated Bim1/EB1 interactions trigger Dam1c ring assembly at the budding yeast outer kinetochore

Dudziak, A., Engelhard, L., Bourque, C., Klink, B. U., Rombaut, P., Kornakov, N., Jänen, K., Herzog, F., Gatsogiannis, C., & Westermann, S. (2021) · The EMBO Journal · doi:10.15252/embj.2021108004 · Cited by 17

Mass Spectrometry Structural Proteomics Enabled by Limited Proteolysis and Cross‐Linking

Lu, H., Zhu, Z., Fields, L. G., Zhang, H., & Li, L. (2024) · Mass Spectrometry Reviews · doi:10.1002/mas.21908 · Cited by 26

How the central domain of dystrophin acts to bridge F-actin to sarcolemmal lipids

Mias‐Lucquin, D., Morais, R. D. S., Cheron, A., Lagarrigue, M., Winder, S. J., Chenuel, T., Pérez, J., Appavou, M., Martel, A., Alviset, G., et al. (2019) · Journal of Structural Biology · doi:10.1016/j.jsb.2019.107411 · Cited by 20

Structural Investigation of Proteins and Protein Complexes by Chemical Cross-Linking/Mass Spectrometry

Piotrowski, C., & Sinz, A. (2018) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-2200-6_8 · Cited by 18

Structural basis for binding diversity of acetyltransferase p300 to the nucleosome

Hatazawa, S., Liu, J., Takizawa, Y., Zandian, M., Negishi, L., Kutateladze, T. G., & Kurumizaka, H. (2022) · iScience · doi:10.1016/j.isci.2022.104563 · Cited by 18

Structural basis of RNA-induced autoregulation of the DExH-type RNA helicase maleless

Jagtap, P. K. A., Muller, M. C., Kiss, A. E., Thomae, A. W., Lapouge, K., Beck, M., Becker, P. B., & Hennig, J. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.10.026 · Cited by 18

Structural and biochemical analyses of the nuclear pore complex component ELYS identify residues responsible for nucleosome binding

Kobayashi, W., Takizawa, Y., Aihara, M., Negishi, L., Ishii, H., & Kurumizaka, H. (2019) · Communications Biology · doi:10.1038/s42003-019-0385-7 · Cited by 18

Phosphorylation‐linked complex profiling identifies assemblies required for Hippo signal integration

Uliana, F., Ciuffa, R., Mishra, R., Fossati, A., Frommelt, F., Keller, S., Mehnert, M., Birkeland, E. S., van Drogen, F., Srejić, N., et al. (2023) · Molecular Systems Biology · doi:10.15252/msb.202211024 · Cited by 21

Biochemical characterisation of Mer3 helicase interactions and the protection of meiotic recombination intermediates

Altmannova, V., Firlej, M., Müller, F., Janning, P., Rauleder, R., Rousova, D., Schäffler, A., Bange, T., & Weir, J. R. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad175 · Cited by 15

Oligomerisation of Synaptobrevin-2 Studied by Native Mass Spectrometry and Chemical Cross-Linking

Wittig, S., Haupt, C., Hoffmann, W., Kostmann, S., Pagel, K., & Schmidt, C. (2018) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-018-2000-4 · Cited by 16

Cross-ID: Analysis and Visualization of Complex XL–MS-Driven Protein Interaction Networks

de Graaf, S. C., Klykov, O. V., van den Toorn, H., & Scheltema, R. A. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00725 · Cited by 15

Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain

Rafiei, A., Tetlalmatzi, S. C., Edrington, C. H., Lee, L., Crowder, D. A., Saltzberg, D. J., Šali, A., Brouhard, G. J., & Schriemer, D. C. (2022) · eLife · doi:10.7554/elife.66975 · Cited by 18

Hydrostatic Pressure Sensing by WNK kinases

Humphreys, J. M., Teixeira, L. R., Akella, R., He, H., Kannangara, A. R., Sekulski, K., Pleinis, J. M., Liwocha, J., Jiou, J., Servage, K. A., et al. (2023) · Molecular Biology of the Cell · doi:10.1091/mbc.e23-03-0113 · Cited by 12

Quantitative Cross-Linking of Proteins and Protein Complexes

Barth, M., & Schmidt, C. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1024-4_26 · Cited by 12

Proxl (Protein Cross-Linking Database): A Public Server, QC Tools, and Other Major Updates

Riffle, M. E., Jaschob, D., Zelter, A., & Davis, T. N. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00726 · Cited by 9

The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex

Hepburn, M., Saltzberg, D. J., Lee, L., Fang, S., Atkinson, C. E., Strynadka, N. C. J., Šali, A., Lees‐Miller, S. P., & Schriemer, D. C. (2021) · Structure · doi:10.1016/j.str.2020.12.006 · Cited by 11

C-Terminal Motifs of the MTW1 Complex Cooperatively Stabilize Outer Kinetochore Assembly in Budding Yeast

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The CroCo cross-link converter: a user-centred tool to convert results from cross-linking mass spectrometry experiments

Bender, J., & Schmidt, C. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz732 · Cited by 10

SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange

Saltzberg, D. J., Hepburn, M., Pilla, K. B., Schriemer, D. C., Lees‐Miller, S. P., Blundell, T. L., & Šali, A. (2019) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2019.09.003 · Cited by 10

ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons

Lubecka, E. A., & Liwo, A. (2021) · Journal of Computational Chemistry · doi:10.1002/jcc.26695 · Cited by 10

Mass spectrometry uncovers intermediates and off-pathway complexes for SNARE complex assembly

Hesselbarth, J., & Schmidt, C. (2023) · Communications Biology · doi:10.1038/s42003-023-04548-0 · Cited by 10

Structure–function analyses of the G729R 2-oxoadipate dehydrogenase genetic variant associated with a disorder of l-lysine metabolism

Zhang, X., Nemeria, N. S., Leandro, J., Houten, S. M., Lazarus, M. B., Gerfen, G. J., Ozohanics, O., Ambrus, A., Nagy, B., Brukh, R., et al. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.012761 · Cited by 9

Structure of E6AP in complex with HPV16-E6 and p53 reveals a novel ordered domain important for E3 ligase activation

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compleXView: a server for the interpretation of protein abundance and connectivity information to identify protein complexes

Solis‐Mezarino, V., & Herzog, F. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx411 · Cited by 8

Biochemical and functional characterization of a meiosis-specific Pch2/ORC AAA+ assembly

Villar-Fernández, M. A., da Silva, R. C., Firlej, M., Pan, D., Weir, E., Sarembe, A., Raina, V. B., Bange, T., Weir, J. R., & Vader, G. (2020) · Life Science Alliance · doi:10.26508/lsa.201900630 · Cited by 7

Identification of the GAox gene family in potato (Solanum tuberosum L.) and its expression analysis in response to drought stress

Jiao, S., Liu, Z., Kang, Y., Zhang, R., Wang, Y., Zhang, J., Liu, Y., & Qin, S. (2024) · Chemical and Biological Technologies in Agriculture · doi:10.1186/s40538-024-00574-0 · Cited by 6

Inert and seed-competent tau monomers suggest structural origins of aggregationPreprint

Mirbaha, H., Chen, D., Morozova, O. A., Ruff, K. M., Sharma, A., Liu, X., Pappu, R. V., Colby, D. W., Mirzaei, H., Joachimiak, Ł. A., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/163394 · Cited by 10

Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosomePreprint

Faull, S. V., Lau, A. M. C., Martens, C., Ahdash, Z., Yébenes, H., Schmidt, C., Beuron, F., Cronin, N., Morris, E. P., & Politis, A. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/483024 · Cited by 6

Affinity-Purification Combined with Crosslinking Mass Spectrometry for Identification and Structural Modeling of Host–Pathogen Protein–Protein Complexes

Happonen, L. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3243-7_12 · Cited by 4

Biological Implications of the Intrinsic Deformability of Human Acetylcholinesterase Induced by Diverse Compounds: A Computational Study

Alvarado, Y. J., González-Paz, L. A., Paz, J. L., Loroño, M., Santiago, J., Lossada, C. A., Vivas, A., Marrero‐Ponce, Y., Martínez-Rios, F., Rodríguez-Lugo, P., et al. (2024) · Biology · doi:10.3390/biology13121065 · Cited by 3

Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass SpectrometryPreprint

Leitner, A., Bonvin, A. M. J. J., Borchers, C. H., Chalkley, R. J., Chamot‐Rooke, J., Combe, C., Cox, J., Dong, M., Fischer, L., Götze, M., et al. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2007.00383 · Cited by 3

Molecular and structural basis of the heterochromatin-specific chromatin remodeling activity by Arabidopsis DDM1Preprint

Osakabe, A., Takizawa, Y., Horikoshi, N., Hatazawa, S., Negishi, L., Berger, F., Kakutani, T., & Kurumizaka, H. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.10.548306 · Cited by 3

Cross-linking mass spectrometry: Workflow enhancements for mapping large-scale interactomes

Balakrishnan, S. M., Nedjadi, T., Alsiary, R., & Ansari, H. R. (2026) · Biophysical Journal · doi:10.1016/j.bpj.2026.05.033 · Cited by 2

Cross-ID: Analysis and Visualization of Complex XL–MS-Driven Protein Interaction Networks

de Graaf, S. C., Klykov, O. V., van den Toorn, H., & Scheltema, R. A. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00725 · Cited by 15

Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures

Kosiński, J., von Appen, A., Ori‬‬, A., Karius, K., Müller, C. W., & Beck, M. (2015) · Journal of Structural Biology · doi:10.1016/j.jsb.2015.01.014 · Cited by 163

xiNET: cross-link network maps with residue resolution

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xiVIEW: Visualisation of Crosslinking Mass Spectrometry Data

Combe, C., Graham, M., Kolbowski, L., Fischer, L., & Rappsilber, J. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168656 · Cited by 103

Using XlinkCyNET to visualize protein cross-links in Cytoscape softwarePreprint

Lima, D. B., Zhu, Y., & Liu, F. (2020) · Research Square · doi:10.21203/rs.3.pex-1172/v1 · Cited by 3