Publications

Selected publications

  • Nichols C, Ng J, Keshu A, … Fraternali F, De Nicola GF. Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1?-IL1R and p38?-TAB1 Complexes. J Med Chem. 2020 Jul 1. doi: 10.1021/acs.jmedchem.0c00403. Online ahead of print.
  • Kepiro IE, Marzuoli I, … Fraternali F, Ryadnov M. Engineering Chirally Blind Protein Pseudocapsids into Antibacterial Persisters [published online ahead of print, 2019 Dec 5]. ACS Nano. 2019;10.1021/acsnano.9b06814. doi:10.1021/acsnano.9b06814
  • Marzuoli I, Margreitter C, Fraternali F. (2019). Lipid Head Group Parameterization for GROMOS 54A8: A Consistent Approach with Protein Force Field Description. J Chem Theory Comput, 15(10):5175-5193. doi: 10.1021/acs.jctc.9b00509.
  • Machpherson JA, Theisen A, Masino L, Fets L, Driscoll PC, Encheva V, Snijders AP, Martin SR, Kleinjung J, Barran PE, Fraternali F, Anastasiou D.
  • (2019). Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation. Elife, pii: e45068. doi: 10.7554/eLife.45068.
  • Ng JCF, Quist J, Grigoriadis A, Malim MH & Fraternali F. (2019). Pan-cancer transcriptomic analysis dissects immune and proliferative functions of APOBEC3 cytidine deaminases, Nucleic Acids Res, 47(3):1178-1194, doi: 10.1093/nar/gky1316.
  • Margreitter C, Lu HC, Townsend C, Stewart A, Dunn-Walters DK & Fraternali F. (2018). BRepertoire: a user-friendly web server for analysing antibody repertoire data. Nucleic Acids Res 46(W1):W264-W270. doi: 10.1093/nar/gky276.
  • Laddach A, Ng JC, Chung SS, Fraternali F. (2018). Genetic variants and protein-protein interactions: a multidimensional network-centric view. Curr Opin Struct Biol. 2018 Jan 4;50:82-90. doi: 10.1016/j.sbi.2017.12.006. [Epub ahead of print]
  • Laddach A, Chung SS, Fraternali F. (2018). Prediction of Protein-Protein Interactions: Looking Through the Kaleidoscope. Encyclopedia of Bioinformatics and Computational Biology. doi: 10.1016/B978-0-12-809633-8.20470-6. [Epub ahead of print]
  • Gehrig S, Macpherson JA, Driscoll PC, Symon AC, Martin SR, MacRae JI, Kleinjung J, Fraternali F. and Anastasiou D. An engineered photoswitchable mammalian pyruvate kinase. FEBS J. 2017 doi: 10.1111/febs.14175. [Epub ahead of print].
  • Laddach A, Gautel M, Fraternali F. TITINdb – a Computational Tool to Assess Titin’s Role as a Disease Gene. Bioinformatics. 2017; btx424. doi: 10.1093/bioinformatics/btx424
  • Townsend CL, Laffy JM, Wu YB, Silva O’Hare J, Martin V, Kipling D, Fraternali F, Dunn-Walters DK. Significant Differences in Physicochemical Properties of Human Immunoglobulin Kappa and Lambda CDR3 Regions. Front Immunol. 2016 Sep 27;7:388.
  • Lu HC, Herrera Braga J, Fraternali F. PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks. Bioinformatics. 2016 Aug 15;32(16):2534-6. doi: 10.1093/bioinformatics/btw153.
  • Chung SS, Pandini A, Annibale A, Coolen AC, Thomas NS, Fraternali F. Bridging topological and functional information in protein interaction networks by short loops profiling. Sci Rep. 2015 Feb 23;5:8540. doi: 10.1038/srep08540.
  • Setta-Kaffetzi N, Simpson MA, Navarini AA, Patel VM, Lu HC, Allen MH, Duckworth M, Bachelez H, Burden AD, Choon SE, Griffiths CE, Kirby B, Kolios A, Seyger MM, Prins C, Smahi A, Trembath RC, Fraternali F, Smith CH, Barker JN, Capon F. AP1S3 mutations are associated with pustular psoriasis and impaired Toll-like receptor 3 trafficking. Am J Hum Genet. 2014 May 1;94(5):790-7. doi: 10.1016/j.ajhg.2014.04.005.
  • Kleinjung J, Fraternali F. Design and application of implicit solvent models in biomolecular simulations. Curr Opin Struct Biol. 2014 25:126-34.
  • Buffa P, Romano C, Pandini A, Massimino M, Tirrò E, Di Raimondo F, Manzella L, Fraternali F, Vigneri PG. BCR-ABL residues interacting with ponatinib are critical to preserve the tumorigenic potential of the oncoprotein. FASEB J. 2014 Mar;28(3):1221-36.
  • Fornili A, Pandini A, Lu HC, Fraternali F. Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles. J Chem Theory Comput. 2013 9(11):5127-5147.
  • Chakroun N, Fornili A, Prigent S, Kleinjung J, Dreiss CA, Rezaei H, Fraternali F. Decrypting Prion Protein Conversion into a ?-Rich Conformer by Molecular Dynamics. J Chem Theory Comput. 2013 9(5):2455-2465.
  • Carlin LM, Evans R, Milewicz H, Fernandes L, Matthews DR, Perani M, Levitt J, Keppler MD, Monypenny J, Coolen T, Barber PR, Vojnovic B, Suhling K, Fraternali F, Ameer-Beg S, Parker PJ, Thomas NS, Ng T. A targeted siRNA screen identifies regulators of Cdc42 activity at the natural killer cell immunological synapse. Sci Signal. 2011 4(201):ra81. doi: 10.1126/scisignal.2001729.
  • Vaz F, Hanenberg H, Schuster B, Barker K, Wiek C, Erven V, Neveling K, Endt D, Kesterton I, Autore F, Fraternali F, Freund M, Hartmann L, Grimwade D, Roberts RG, Schaal H, Mohammed S, Rahman N, Schindler D, Mathew CG. Mutation of the RAD51C gene in a Fanconi anemia-like disorder. Nat Genet. 2010 42(5):406-9.
  • De Simone A, Corrie JE, Dale RE, Irving M, Fraternali F. Conformation and dynamics of a rhodamine probe attached at two sites on a protein: implications for molecular structure determination in situ. J Am Chem Soc. 2008
  • De Simone A, Dodson GG, Verma CS, Zagari A, Fraternali F. Prion and water: tight and dynamical hydration sites have a key role in structural stability. Proc Natl Acad Sci U S A. 2005 May 24;102(21):7535-40.