ARTICLES
2021
43. L. S. P. Rudden, S. C. Musson, J. L. P. Benesch, M. T. Degiacomi ✉ (2021). Biobox: a toolbox for biomolecular modelling, Bioinformatics
42. M.T. Degiacomi ✉, S. Tian, H.C. Greenwell, V. Erastova (2021). DynDen: Assessing convergence of molecular dynamics simulations of interfaces, Computer Physics Communications
41. L.S.P. Rudden & M.T. Degiacomi ✉ (2021), Transmembrane protein docking with JabberDock, Journal of Chemical Information and Modelling
40. V.K. Ramaswamy, S.C. Musson, C.G. Willcocks, M.T. Degiacomi ✉ (2021). Learning protein conformational space with convolutions and latent interpolations, Physical Review X 11
39. A. Olerinyova, A. Sonn-Segev, J. Gault, C. Eichmann, J. Schimpf, A.H. Kopf, L.S.P. Rudden, D. Ashkinadze, R. Bomba, J. Greenwald, M.T. Degiacomi, J.A. Killian, T. Friedrich, R. Riek, W.B. Struwe, P. Kukura (2021). Mass Photometry of Membrane Proteins, Chem 7(1)
2020
38. A. Leach, L.S.P. Rudden, S. Bond-Taylor, J.C. Brigham, M.T. Degiacomi ✉, C.G. Willcocks (2020). Shape tracing: An extension of sphere tracing for 3D non-convex collision in protein docking, 2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE)
37. T. Allison, P. Barran, S. Cianferani, M.T. Degiacomi, V. Gabelica, R. Grandori, E. Marklund, T. Menneteau, L. Migas, A. Politis, M. Sharon, F. Sobott, K. Thalassinos, J.L.P. Benesch (2020). Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology, Analytical Chemistry
36. T. Allison, P. Barran, J.L.P. Benesch, S. Cianferani, M.T. Degiacomi, V. Gabelica, R. Grandori, E. Marklund, T. Menneteau, L. Migas, A. Politis, M. Sharon, F. Sobott, K. Thalassinos (2020). Software requirements for the analysis and interpretation of native mass spectrometry data, Analytical Chemistry
35. M. Landreh, C. Sahin, J. Gault, S. Sadeghi, C.L. Drum, P. Uzdavinys, D. Drew, T.M. Allison, M.T. Degiacomi ✉, E.G. Marklund (2020). Predicting the shapes of protein complexes through collision cross section measurements and database searches, Analytical Chemistry
2019
34. L.P. Rudden & M.T. Degiacomi ✉ (2019), Protein docking using a single representation for protein surface, electrostatics and local dynamics. Journal of Chemical Theory and Computation
33. M.P. Collier, T.R. Alderson, C.P. de Villiers, D. Nicholls, H.Y. Gastall, T.M. Allison, M.T. Degiacomi, H. Jiang, G. Mlynek, D.O. Fürst, P.F.M. van der Ven, K. Djinovic-Carugo, A.J. Baldwin, H. Watkins, K. Gehmlich, J.L.P. Benesch. (2019). HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C. Science Advances. 5(5)
32. M.T. Degiacomi ✉ (2019), Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space. Structure. datasets
31. Y.A. Lyon, M.P. Collier, D.L. Riggs, M.T. Degiacomi, J.L.P. Benesch, R.R. Julian (2019). Structural and functional consequences of age-related isomerization in α-crystallins. Journal of Biological Chemisty. Editors’ Pick
30. M.T. Degiacomi ✉ (2019). On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies. Journal of the American Mass Spectrometry Society
2018
29. Santhanagopalan I., Degiacomi M.T., Shepherd D.A., Hochberg G.K.A., Benesch J.L.P., Vierling E., (2018). It takes a dimer to tango: Oligomeric small heat shock proteins dissociate to capture substrate, Journal of Biological Chemisty
28. Finelli M.J., Aprile D., Castroflorio E., Jeans A., Moschetta M., Chessum L., Degiacomi M.T., Grasegger J., Lupien-Meilleur A., Bassett A., Rossignol E., Campeau P.M., Bowl M.R., Benfenati F., Fassio A., Oliver P.L. (2018). The epilepsy-associated protein TBC1D24 is required for normal development, survival and vesicle trafficking in mammalian neurons. Human Molecular Genetics 28 (4), 584–597
27. Liko, I., Degiacomi, M.T., Lee, S., Newport, T.D., Gault, J., Reading, E., Hopper, J.T.S., Housden, N.G., White, P., Colledge, M., Sula, A., Wallace, B.A., Kleanthous, C., Stansfeld, P.J., Bayley, H., Benesch, J.L.P., Allison, T.M., Robinson, C.V., (2018). Lipid binding attenuates channel closure of the outer membrane protein OmpF. Proceedings of the National Academy of Sciences of the United States of America, 115 (26), 6691-6696
26. Hochberg, G.K.A., Shepherd, D.A., Marklund, E.G., Santhanagoplan, I., Degiacomi M.T., Laganowsky, A., Allison, T.M., Basha, E., Marty, M.T., Galpin, M.R., Struwe, W.B., Baldwin, A.J., Vierling, E., Benesch, J.L.P. (2018). Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions, Science, 359 (6378), 930-935. datasets
2017
25. Erastova, V. *, Degiacomi, M.T. *, Fraser, D.G., Greenwell, H.C. (2017). Mineral surface control for origin of prebiotic peptides, Nature Communications 8 (1): 2033 datasets.
24. Degiacomi, M.T. ✉, Schmidt, C. , Baldwin, A.J., Benesch, J.L.P. (2017). Accommodating Protein Dynamics in the Modeling of Chemical Crosslinks, Structure, 25(11), 1751-1757. datasets
23. Pritisanac, I., Degiacomi, M.T., Alderson, T.R., Carneiro, M.G., AB, E., Siegal, Gregg & Baldwin, Andrew J (2017). Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory. Journal of the American Chemical Society
22. Tamò, G., Maesani, A., Träger, S., Degiacomi, M.T., Floreano, D. & Dal Peraro, M. (2017). Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies. Scientific reports 7(1): 235.
21. Landreh, M., Marklund, E.G., Uzdavinys, P., Degiacomi, M.T., Coincon, M., Gault, J., Gupta, K., Liko, I., Benesch, J.L.P., Drew, D. & Robinson, C.V. (2017). Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters. Nature Communications 8.
20. Hopper, J.T.S., Ambrose, S., Grant, O.C., Krumm, S.A., Allison, T.M., Degiacomi, M.T., Tully, M.D., Pritchard, L.K., Ozorowski, G., Ward, A.B., Crispin, M., Doores, K.J., Woods, R.J., Benesch, J.L.P., Robinson, C.V. & Struwe, W.B. (2017). The Tetrameric Plant Lectin BanLec Neutralizes HIV through Bidentate Binding to Specific Viral Glycans. Structure 25(5): 773-782.e5.
19. Erastova, V., Degiacomi, M. T., O’Hare, D. & Greenwell, H.C. (2017). Understanding surface interactions in aqueous miscible organic solvent treated layered double hydroxides. RSC Advances 7(9): 5076-5083.
2016
18. McDowell, M.A., Marcoux, J., Mcvicker, G., Johnson, S., Fong, Y.H., Stevens, R., Bowman, L.A.H., Degiacomi, M.T., Yan, J., Wise, A., Friede, M.E., Benesch, J.L.P., Deane, J.E., Tang, C.M., Robinson, C.V. & Lea, S.M. (2016). Characterisation of ShigellaSpa33 and ThermotogaFliM/N reveals a new model for C-ring assembly in T3SS. Molecular Microbiology 99(4): 749-766.
17. Liko, I., Degiacomi, M.T., Mohammed, S., Yoshikawa, S., Schmidt, C. & Robinson, C.V. (2016). Dimer interface of Bovine cytochrome c oxidase is influenced by local posttranslational modifications and lipid binding. Proceedings of the National Academy of Sciences of the United States of America 113(29): 8230-8235.
16. Degiacomi, M.T.*✉, Erastova, V. * & Wilson, M.R. (2016). Easy creation of polymeric systems for molecular dynamics with Assemble!. Computer Physics Communications 202: 304-309.
15. Degiacomi, M.T. ✉ & Benesch, J.L.P. (2016). EM∩IM: Software for relating ion mobility mass spectrometry and electron microscopy data. Analyst 141(1): 70-75.
2015
14. Marcoux, J., Mangione, P.P., Porcari, R., Degiacomi, M.T., Verona, G., Taylor, G.W., Giorgetti, S., Raimondi, S., Sanglier-Cianférani, S., Benesch, J.L., Cecconi, C., Naqvi, M.M., Gillmore, J.D., Hawkins, P.N., Stoppini, M., Robinson, C.V., Pepys, M.B. & Bellotti, V. (2015). A novel mechano-enzymatic cleavage mechanism underlies transthyretin amyloidogenesis. EMBO Molecular Medicine 7(10): 1337-1349.
13. Bechara, C., Nöll, A., Morgner, N., Degiacomi, M.T., Tampé, R. & Robinson, C.V. (2015). A subset of annular lipids is linked to the flippase activity of an ABC transporter. Nature Chemistry 7(3): 255-262.
12. Marklund, E.G., Degiacomi, M.T., Robinson, C.V., Baldwin, A.J. & Benesch, J.L.P. (2015). Collision cross sections for structural proteomics. Structure 23(4): 791-799.
2014
11. Laganowsky, A., Reading, E., Allison, T.M., Ulmschneider, M.B., Degiacomi, M.T., Baldwin, A.J. & Robinson, C.V. (2014). Membrane proteins bind lipids selectively to modulate their structure and function. Nature 510(7503): 172-175.
10. Spiga, E.*, Degiacomi, M.T. * & Dal Peraro, M. (2014). New strategies for integrative dynamic modeling of macromolecular assembly, in Advances in Protein Chemistry and Structural Biology 96: 77-111.
9. Bovigny, C., Degiacomi, M.T., Lemmin, T., Dal Peraro, M. & Stenta, M. (2014). Reaction mechanism and catalytic fingerprint of allantoin racemase. Journal of Physical Chemistry B 118(27): 7457-7466.
2013 and earlier
8. Hofmeyer, T., Schmelz, S., Degiacomi, M.T., Dal Peraro, M., Daneschdar, M., Scrima, A., Van Den Heuvel, J., Heinz, D.W. & Kolmar, H. (2013). Arranged sevenfold: Structural insights into the C-terminal oligomerization domain of human C4b-binding protein. Journal of Molecular Biology 425(8): 1302-1317.
7. Spiga, E., Alemani, D., Degiacomi, M.T., Cascella, M. & Peraro, M.D. (2013). Electrostatic-consistent coarse-grained potentials for molecular simulations of proteins. Journal of Chemical Theory and Computation 9(8): 3515-3526.
6. Kudryashev, M., Stenta, M., Schmelz, S., Amstutz, M., Wiesand, U., Castaño-Díez, D., Degiacomi, M.T., Münnich, S., Bleck, C.K.E., Kowal, J., Diepold, A., Heinz, D.W., Dal Peraro, M., Cornelis, G.R. & Stahlberg, H. (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife 2013(2).
5. Degiacomi, M.T. & Dal Peraro, M. (2013). Macromolecular symmetric assembly prediction using swarm intelligence dynamic modeling. Structure 21(7): 1097-1106.
4. Degiacomi, M.T.*, Iacovache, I.*, Pernot, L., Chami, M., Kudryashev, M., Stahlberg, H., Van Der Goot, F.G. & Dal Peraro, M. (2013). Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism. Nature Chemical Biology 9(10): 623-629. [News and Views article]
3. Iacovache, I. *, Degiacomi, M.T. *, Pernot, L., Ho, S., Schiltz, M., Dal Peraro, M. & van der Goot, F.G. (2011). Dual chaperone role of the c-terminal propeptide in folding and oligomerization of the pore-forming toxin aerolysin. PLoS Pathogens 7(7).
2. Wagner, S., Sorg, I., Degiacomi, M., Journet, L., Peraro, M.D. & Cornelis, G.R. (2009). The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome. Molecular Microbiology 71(3): 692-701.
1. S. Gowal, M. De Giacomi & J.-Y. Le Boudec (2007). Comment on: A validated mathematical model of cell-mediated immune response to tumor growth [1]. Cancer Research 67(17): 8419-8420.
BOOK CHAPTERS
2. E. G. Marklund, M. T. Degiacomi, A. Politis & M. Landreh (2021). Chapter 8: CCS for Modelling 3D Structures, in Ion Mobility-Mass Spectrometry: Fundamentals and Applications, Royal Society of Chemistry
1. I. Iacovache, M.T. Degiacomi & F.G. van der Goot (2012). 5.9. Pore-forming toxins, in Comprehensive Biophysics, Elsevier
PATENTS
Method for processing nuclear magnetic resonance (NMR) spectroscopic data European patent, US patent
MEDIA
Our research on machine learning to sample protein conformational spaces featured in the news of the SoftComp network (2021)
Scientist Next Door, the virtual public engagement initiative we co-funded, featured in the Northern Echo: “Scientists help children learn during lockdown” (2020)
Our proposed model for abiogenesis featured in an interview on RT: ‘How did life form from rocks?’ Protein puzzle reveals secrets of Earth’s evolution (2018)
Research on injectisome highlighted in BBC “Dara O’Brian’s Science Club” episode “Size Matters” and Science Daily (2013)
Research on aerolysin mode of action featured in the international press, such as BBC Mundo, La Voz de Galicia, Wiener Zeitung, Science Daily, 24 Heures, Le Matin and Tages Anzeiger, and a radio interview (in French) at the Swiss National Radio, RTS (2013)
Degiacomi research group 