Publications

Recent 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.
Complete list
  • 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.
  • Kelly JR, Martini S, … Fraternali F, Parker PJ, Soliman TN. The Aurora B specificity switch is required to protect from non-disjunction at the metaphase/anaphase transition. Nat Commun. 2020 Mar 13;11(1):1396. doi: 10.1038/s41467-020-15163-6.
  • Haga RB, Garg R, Collu F, … Fraternali F, Ridley AJ. RhoBTB1 interacts with ROCKs and inhibits invasion. Biochem J. 2019 Sep 13;476(17):2499-2514. doi: 10.1042/BCJ20190203.
  • 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
  • Jimeno R, Lebrusant-Fernandez M, Margreitter C, Lucas B, Veerapen N, Besra GS, Fraternali F, Spencer J, Anderson G, Barral P. (2019). Tissue-specific shaping of the TCR repertoire and antigen specificity of iNKT cells. eLife, pii: e51663. doi: 10.7554/eLife.51663.
  • 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.
  • Abis G, Charles RL, Kopec J, Yue WW, Atkinson RA, Bui TTT, Lynham S, Popova S, Sun YB, Fraternali F, Eaton P & Conte MR. (2019). 15-deoxy-?12,14-Prostaglandin J2 inhibits human soluble epoxide hydrolase by a dual orthosteric and allosteric mechanism, Communications Biology, 2:188.
  • 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.
  • Macpherson JA, Theisen A, Masino L … Kleinjung J, Perdita EB, Fraternali F & Anastasiou D. (2018). Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation. bioRxivhttps://www.biorxiv.org/content/early/2018/07/26/378133
  • Chung SS, Laddach A, Thomas NSB & Fraternali F. (2018). Short loop motif profiling of protein interaction networks in acute myeloid leukaemia. bioRxivhttps://www.biorxiv.org/content/early/2018/04/25/306886
  • 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.
  • Milano G, Marzuoli I, Lorenz CD, Fraternali F. Self-assembly at the multi-scale level: challenges and new avenues for inspired synthetic biology modelling. In Ryadnov M, Brunsveld L, Suga H (eds.), Synthetic Biology: Volume 2; pp. 35-64. London: The Royal Society of Chemistry. doi: 10.1039/9781782622789-00035. (2018).
  • Laddach A, Ng JC, Chung SS, Fraternali F. 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] (2018).
  • Laddach A, Chung SS, Fraternali F. 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] (2018).
  • Tiberti M, Pandini A, Fraternali F, Fornili A. In silico identification of rescue sites by double force scanning. Bioinformatics. doi: 10.1093/bioinformatics/btx515. [Epub ahead of print] (2017).
  • Pappalardo, M., Collu, F., Macpherson, J., Michaelis, M., Fraternali, F., & Wass, M. N. Investigating Ebola virus pathogenicity using molecular dynamics. BMC Genomics, 18(S5), 566. doi: 10.1186/s12864-017-3912-2. (2017).
  • 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. 33(21):3482–3485. doi: 10.1093/bioinformatics/btx424 (2017).
  • Schmidt C, Macpherson JA, Lau AM, Tan KW, Fraternali F and Politis A. Surface Accessibility and Dynamics of Macromolecular Assemblies Probed by Covalent Labeling Mass Spectrometry and Integrative Modeling. Chem. 89(3) 1459–1468 (2017).
  • Carluccio C, Fraternali F, Salvatore F, Fornili A and Zagari A. Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase. Biomol. Str. Dyn. 34(3) 497–507 (2016).
  • Laffy JM, Dodev T, Macpherson JA, Townsend C, Lu HC, Dunn-Walters D and Fraternali F. Promiscuous antibodies characterised by their physico-chemical properties: From sequence to structure and back. Biophys. Mol. Biol. S0079-6107(16) 30047–5 (2016).
  • Lu HC and Herrera Braga F J amd Fraternali. PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks. Bioinformatics 32(16) 2534–2536 (2016).
  • Martin VG, Wu YB, Townsend CL, Lu GH, O’Hare JS, Mozeika A, Coolen AC, Kipling D, Fraternali F and Dunn-Walters DK. Transitional B Cells in Early Human B Cell Development – Time to Revisit the Paradigm? Immunol. 7 546 (2016).
  • Townsend CL, Laffy JM, Wu YB, Silva O’Hare J, Martin V, Kipling D, Fraternali F and Dunn-Walters DK. Significant Differences in Physicochemical Properties of Human Immunoglobulin Kappa and Lambda CDR3 Regions. Immunol. 7 388 (2016).
  • Tremonte P, Succi M, Coppola R, Sorrentino E, Tipaldi L, Picariello G, Pannella G and Fraternali F. Homology-Based Modeling of Universal Stress Protein from Listeria innocua Up-Regulated under Acid Stress Conditions. Microbiol. 7 1998 (2016).
  • Botten D, Fugallo G, Fraternali F and Molteni C. Structural Properties of Green Tea Catechins. Phys. Chem. B 119(40) 12860–12867 (2015).
  • Chung SS, Pandini A, Annibale A, Coolen ACC, Thomas NSB and Fraternali F. Bridging topological and functional information in protein interaction networks by short loops profiling. Reports 5 8540 (2015).
  • Collu F, Spiga E, Lorenz CD and Fraternali F. Assembly of Influenza Hemagglutinin Fusion Peptides in a Phospholipid Bilayer by Coarse-grained Computer Simulations. Frontiers Mol. Biosci. 2 66 (2015).
  • Lu Hc, Chung SS, Fornili A and Fraternali F. Anatomy of protein disorder, flexibility and disease-related mutations. Frontiers Mol. Biosci. 2 47 (2015).
  • Prescott NJ, Lehne B, Stone K, Lee JC, Taylor K, Knight J, Papouli E, Mirza MM, Simpson MA, Spain SL, Lu G, Fraternali F et al. Pooled sequencing of 531 genes in inflammatory bowel disease identifies an associated rare variant in BTNL2 and implicates other immune related genes. PLoS Genetics 11(2) e1004955 (2015).
  • Buffa P, Romano C, Pandini A, Massimino M, Tirr`o E, Di Raimondo F, Manzella L, Fraternali F and Vigneri PG. BCR-ABL residues interacting with ponatinib are critical to preserve the tumorigenic potential of the oncoprotein. FASEB J. 28(3) 1221–1236 (2014).
  • Haria NR, Monticelli L, Fraternali F and Lorenz CD. Plasticity and conformational equilibria of influenza fusion peptides in model lipid bilayers. Biophys. Acta 1838(4) 1169–1179 (2014).
  • Kleinjung J and Fraternali F. Design and Application of Implicit Solvent Models in Biomolecular Simulations. Op. Str. Biol. 25 126–134 (2014).
  • Scharner J, Lu Hc, Fraternali F, Ellis JA and Zammit PS. Mapping disease-related missense mutations in the immunoglobulin-like fold domain of lamin A/C reveals novel genotype-phenotype associations for laminopathies. Proteins 82(6) 904–915 (2014).
  • Setta-Kaffetzi N, Simpson MA, Navarini AA, Patel VM, Lu Hc, Allen MH, Duckworth M, Bachelez H, Burden AD, Choon SE, Griffiths CEM, Kirby B et al. AP1S3 Mutations Are Associated with Pustular Psoriasis and Impaired Toll-like Receptor 3 Trafficking. J. Hum. Gen. 94(5) 790–797 (2014).
  • Autore F, Pfuhl M, Quan X,Williams A, Roberts RG, Shanahan CM and Fraternali F. Large-scale modelling of the divergent spectrin repeats in nesprins: giant modular proteins. PloS One 8(5) e63633 (2013).
  • Botten D, Fugallo G, Fraternali F and Molteni C. A computational exploration of the interactions of the green tea polyphenol (-)-Epigallocatechin 3-Gallate with cardiac muscle troponin C. PloS One 8(7) e70556 (2013).
  • Carluccio C, Fraternali F, Salvatore F, Fornili A and Zagari A. Structural Features of the Regulatory ACT Domain of Phenylalanine Hydroxylase. PloS One 8(11) e79482 (2013).
  • Chakroun N, Fornili A, Prigent S, Kleinjung J, Dreiss CA, Rezaei H and Fraternali F. Decrypting Prion Protein Conversion into a ?-Rich Conformer by Molecular Dynamics. Chem. Theor. Comp. 9(5) 2455–2465 (2013).
  • Fornili A, Pandini A, Lu Hc and Fraternali F. Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles. Chem. Theor. Comp. 9(11) 5127–5147 (2013).
  • Kar G, Keskin O, Fraternali F and Gursoy A. Emerging role of the ubiquitinproteasome system as drug targets. Pharm. Design 19(18) 3175–3189 (2013).
  • Lu Hc, Fornili A and Fraternali F. Protein-protein interaction networks studies and importance of 3D structure knowledge. Expert Review of Proteomics 10(6) 511–520 (2013).
  • Pagano B, Jama A, Martinez P, Akanho E, Bui TTT, Drake AF, Fraternali F and Nikolova PV. Structure and Stability Insights into Tumour Suppressor p53 Evolutionary Related Proteins. PloS One 8(10) e76014 (2013).
  • Pandini A, Fornili A, Fraternali F and Kleinjung J. GSATools: analysis of allosteric communication and functional local motions using a Structural Alphabet. Bioinformatics 29(16) 2053–2055 (2013).
  • Fornili A, Autore F, Chakroun N, Martinez P and Fraternali F. Protein-water interactions in MD simulations: POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sites. Mol. Biol. 819 375–392 (2012).
  • Kleinjung J and Fraternali F. Urea-Water Solvation Forces on Prion Structures. Chem. Theor. Comp. 8(10) 3977–3984 (2012).
  • Kleinjung J, Scott WRP, Allison JR, van Gunsteren WF and Fraternali F. Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations. Chem. Theor. Comp. 8(7) 2391–2403 (2012).
  • Pandini A, Fornili A, Fraternali F and Kleinjung J. Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics. FASEB J. 26(2) 868–881 (2012).
  • Satoh T, Smith A, Sarde A, Lu Hc, Mian S, Mian S, Trouillet C, Mufti G, Emile JF, Fraternali F, Donadieu J and Geissmann F. B-RAF mutant alleles associated with Langerhans cell histiocytosis, a granulomatous pediatric disease. PloS One 7(4) e33891 (2012).
  • Allison JR, Boguslawski K, Fraternali F and van Gunsteren WF. A refined, efficient mean solvation force model that includes the interior volume contribution. Phys. Chem. B 115(15) 4547–4557 (2011).
  • Carlin LM, Evans R, Milewicz H, Fernandes L, Matthews DR, Perani M, Levitt J, Keppler MD, Monypenny J, Coolen T, Barber PR, Vojnovic B et al. A targeted siRNA screen identifies regulators of Cdc42 activity at the natural killer cell immunological synapse. Science Signaling 4(201) ra81–ra81 (2011).
  • Fruhwirth GO, Fernandes LP, Weitsman G, Patel G, Kelleher M, Lawler K, Brock A, Poland SP, Matthews DR, Keri G, Barber PR, Vojnovic B et al. How F¨orster resonance energy transfer imaging improves the understanding of protein interaction networks in cancer biology. Phys. Chem. 12 442–461 (2011).
  • McCole RB, Loughran NB, Chahal M, Fernandes LP, Roberts RG, Fraternali F, O’Connell MJ and Oakey RJ. A case-by-case evolutionary analysis of four imprinted retrogenes. Evolution 65(5) 1413–1427 (2011).
  • Schroder S, Fraternali F, Quan X, Scott DJ, Qian F and M P. When a module is not a domain – the case of the REJ module and the redefinition of the architecture of polycystin-1. Biochem J 435(3) 651–660 (2011).
  • Autore F, Bergeron JRC, Malim MH, Fraternali F and Huthoff H. Rationalisation of the differences between APOBEC3G structures from crystallography and NMR studies by molecular dynamics simulations. PLoS One 5 e11515 (2010).
  • Autore F, Pagano B, Fornili A, Rittinger K and Fraternali F. In silico phosphorylation of the autoinhibited form of p47(phox): insights into the mechanism of activation. Biophys J 99 3716–3725 (2010).
  • Chakroun N, Prigent S, Dreiss CA, Noinville S, Chapuis C, Fraternali F and Rezaei H. The oligomerization properties of prion protein are restricted to the H2H3 domain. FASEB J. 24 3222–3231 (2010).
  • Fernandes LP, Annibale A, Kleinjung J, Coolen ACC and Fraternali F. Protein networks reveal detection bias and species consistency when analysed by informationtheoretic methods. PLoS One 5 e12083 (2010).
  • Merabet A, Houlleberghs H, Maclagan K, Akanho E, Bui TTT, Pagano B, Drake AF, Fraternali F and Nikolova PV. Mutants of the tumour suppressor p53 L1 loop as second-site suppressors for restoring DNA binding to oncogenic p53 mutations: structural and biochemical insights. Biochem J 427 225–236 (2010).
  • Vaz F, Hanenberg H, Schuster B, Barker K, Wiek C, Erven V, Neveling K, Endt D, Kesterton I, Autore F, Fraternali F, Freund M et al. Mutation of the RAD51C gene in a Fanconi anemia-like disorder. Genet. 42 406–409 (2010).
  • Annibale A, Coolen ACC, Fernandes LP, Fraternali F and Kleinjung J. Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure. Journal of Physics A: Math. Theor. 42 485001 (2009).
  • Huthoff H, Autore F, Gallois-Montbrun S, Fraternali F and Malim MH. RNAdependent oligomerization of APOBEC3G is required for restriction of HIV-1. PLoS Pathog. 5 e1000330 (2009).
  • Nicastro G, Masino L, Esposito V, Menon R, Simone AD, Fraternali F and Pastore A. Josephin domain of ataxin-3 contains two distinct ubiquitin-binding sites. Biopolymers 91 1203–1214 (2009).
  • Coluzza I, De Simone A, Fraternali F and Frenkel D. Multi-scale simulations provide supporting evidence for the hypothesis of intramolecular protein translocation in GroEL/GroES complexes. PLoS Comput. Biol. 4 e1000006 (2008).
  • De Simone A, Corrie JE, Dale RE, Irving M and Fraternali F. Conformation and dynamics of a rhodamine probe attached at two sites on a protein: implications for molecular structure determination in situ. Am. Chem. Soc. 130 17120–17128 (2008).
  • Festa G, Autore F, Fraternali F, Giardina P and Sannia G. Development of new laccases by directed evolution: functional and computational analyses. Proteins 72 25–34 (2008).
  • Pagano B, Mattia CA, Cavallo L, Uesugi S, Giancola C and Fraternali F. Stability and cations coordination of DNA and RNA 14-mer G-quadruplexes: a multiscale computational approach. Phys. Chem. B 112 12115–12123 (2008).
  • Patel S, Bui TTT, Drake AF, Fraternali F and Nikolova PV. The p73 DNA binding domain displays enhanced stability relative to its homologue, the tumor suppressor p53, and exhibits cooperative DNA binding. Biochemistry 47 3235–3244 (2008).
  • Patel S, George R, Autore F, Fraternali F, Ladbury JE and V NP. Molecular interactions of ASPP1 and ASPP2 with the p53 protein family and the apoptotic promoters PUMA and Bax. Acids Res. 36 5139–5151 (2008).
  • Rabello S, Coolen ACC, Perez-Vicente CJ and Fraternali F. A solvable model of the genesis of amino-acid sequences via coupled dynamics of folding and slow genetic variation. Phys. A: Math. Theor. 41 285004 (2008).
  • Virno A, Mayol L, Ramos A, Fraternali F, Pagano B and Randazzo A. Structural insight into the hTERT intron 6 sequence d(GGGGTGAAAGGGG) from 1H-NMR study. Nucleosides Nucleotides Nucleic Acids 26 1133–1137 (2008).
  • Autore F, Melchiorre S, Kleinjung J, Morgan WD and Fraternali F. Interaction of malaria parasite-inhibitory antibodies with the merozoite surface protein MSP119 by computational docking. Proteins 66 513–527 (2007).
  • Azzu V, Yadin D, Patel H, Fraternali F, Chantler PD and Molloy JE. Calcium regulates scallop muscle by changing myosin flexibility. Biophys. J. 35 302–312 (2007).
  • Pandini A, Bonati L, Fraternali F and Kleinjung J. MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database. Bioinformatics 23 515–516 (2007).
  • De Simone A, Dodson GG, Fraternali F and Zagari A. Water molecules as structural determinants among prions of low sequence identity. FEBS Lett. 580 2488–2494 (2006).
  • De Simone A, Spadaccini R, Temussi PA and Fraternali F. Toward the understanding of MNEI sweetness from hydration map surfaces. J. 90 3052–3061 (2006).
  • Mollica L, Fraternali F and Musco G. Interactions of the C2 domain of human factor V with a model membrane. Proteins 64 363–375 (2006).
  • Taylor WR, Lin K, Klose D, Fraternali F and Jonassen I. Dynamic domain threading. Proteins 64 601–614 (2006).
  • De Simone A, Dodson GG, Verma CS, Zagari A and Fraternali F. Prion and water: tight and dynamical hydration sites have a key role in structural stability. Natl. Acad. Sci. USA 102 7535–7540 (2005).
  • Kleinjung J and Fraternali F. Molecular simulations in structure predictions. In Jorde LB, editor, Encyclopedia of Genetics, Genomics, Proteomics and bioinformatics, 28.14. John Wiley and Sons, Ltd (2005).
  • Kleinjung J and Fraternali F. POPSCOMP: an automated interaction analysis of biomolecular complexes. Nucleic Acids Res. 33 W342–W346 (2005).
  • Vaccaro L, Cross KJ, Kleinjung J, Straus SK, Thomas DJ, Wharton SA, Skehel JJ and Fraternali F. Plasticity of influenza haemagglutinin fusion peptides and their interaction with lipid bilayers. J. 88 25–36 (2005).
  • Vaccaro L, Cross KJ, Wharton SA, Skehel JJ and Fraternali F. Aspects of the fusogenic activity of influenza haemagglutinin peptides by molecular dynamics simulations. In Fischer WB, editor, Viral membrane proteins: structure, function, and drug design, 65–75. Kluwer Academic / Plenum Publisher (2005).
  • Cavallo L, Moore MH, Corrie JET and Fraternali F. Quantum mechanics calculations on rhodamine dyes require inclusion of solvent water for accurate representation of the structure. Phys. Chem. A 108 7744–7751 (2004).
  • Eberini I, Baptista AM, Gianazza E, Fraternali F and Beringhelli T. Reorganization in apo- and holo–lactoglobulin upon protonation of Glu89: molecular dynamics and pKa calculations. Proteins 54 744–758 (2004).
  • Fraternali F and Kleinjung J. Molecular simulations in structural genomics. Enzyclopedia of Genetics, Genomics, Proteomics and Bioinformatics 82 904–915 (2004).
  • Mazzini S, Bellucci MC, Dallavalle S, Fraternali F and Mondelli R. Mode of binding of camptothecins to double helix oligonucleotides. Biomol. Chem. 2 505–513 (2004).
  • Cavallo L, Kleinjung J and Fraternali F. POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level. Nucleic Acids Res. 31 3364–3366 (2003).
  • Fraternali F, Cavallo L and Musco G. Effects of pathological mutations on the stability of a conserved amino acid triad in retinoschisin. FEBS Lett. 544 21–26 (2003).
  • Kleinjung J, Fraternali F, Martin SR and Bayley PM. Thermal unfolding simulations of apo-calmodulin using leap-dynamics. Proteins 50 648–656 (2003).
  • Mombelli E, Morris R, Taylor W and Fraternali F. Hydrogen-bonding propensities of sphingomyelin in solution and in a bilayer assembly: a molecular dynamics study. Biophys J. 84 1507–1517 (2003).
  • Fraternali F and Cavallo L. Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome. Nucleic Acids Res. 30 2950–2960 (2002).
  • Amodeo P, Fraternali F, Lesk AM and Pastore A. Modularity and homology: modelling of the titin type I modules and their interfaces. Mol. Biol. 311 283–296 (2001).
  • Falcigno L, Fraternali F, Manduca DM, D’Auria G, Simonetti M, Di Bello C and Paolillo L. A conformational study in solution of pro-somatostatin fragments by NMR and computational methods. Pept. Sci. 4 305–318 (2000).
  • Fraternali F, Amodeo P, Musco G, Nilges M and Pastore A. Exploring protein interiors: the role of a buried histidine in the KH module fold. Proteins 34 484–496 (2000).
  • Fraternali F, Do QT, Doan BT, Atkinson RA, Palmas P, Sklenar V, Safar P, Wildgoose P, Strop P and Saudek V. Mapping the active site of factor Xa by selective inhibitors: an NMR and MD study. Proteins 30 264–274 (2000).
  • Kleinjung J, Bayley P and Fraternali F. Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution. FEBS Lett. 470 257–262 (2000).
  • Adinolfi S, Bagni C, Castiglione Morelli MA, Fraternali F, Musco G and Pastore A. Novel RNA-binding motif: the KH module. Biopolymers 51 153–164 (1999).
  • De Marino S, Morelli MA, Fraternali F, Tamborini E, Musco G, Vrtala S, Dolecek C, Arosio P, Valenta R and Pastore A. An immunoglobulin-like fold in a major plant allergen: the solution structure of Phl p 2 from timothy grass pollen. Structure 7 943–952 (1999).
  • Fraternali F, Amodeo P, Musco G, Nilges M and Pastore A. Exploring protein interiors: the role of a buried histidine in the KH module fold. Proteins: Struc. Func. Gen. 34 484–496 (1999).
  • Fraternali F, Anselmi C and Temussi PA. Neurologically active plant compounds and peptide hormones: a chirality connection. FEBS Lett. 448 217–220 (1999).
  • Fraternali F and Pastore A. Modularity and homology: modelling of the type II module family from titin. Mol. Biol. 290 581–593 (1999).
  • Cavallo L and Fraternali F. A molecular dynamics study of the first five generations of poly(propyleneimine) dendrimers modified with N-t-Boc-L-phenylalanine. Eur. J. 4 927–934 (1998).
  • Doan BT, Fraternali F, Do QT, Atkinson RA, Palmas P, Sklenar V, Wildgoose P, Strop P and Saudek V. NMR and MD study of the active site of factor Xa by selective inhibitors. Chem. Phys. 95 443–446 (1998).
  • Crescenzi O, Fraternali F, Picone D, Tancredi T, Balboni G, Guerrini R, Lazarus LH, Salvadori S and Temussi PA. Design and solution structure of a partially rigid opioid antagonist lacking the basic center – models of antagonism. J. Biochem. 247 66–73 (1997).
  • Fraternali F and Wipff G. Binding of NR4+ ammonium ions by a bridged calix[6]arene in chloroform. An MD investigation. Chim. Int. Ed. 93 376–384 (1997).
  • Fraternali F and Wipff G. Interaction of the t-butyl-calix[4]arene anion with ammonium cations in acetonitrile: host-guest or exo counterions? A molecular dynamics investigation. Incl. Phenom. Mol. Recog. 28 63–78 (1997).
  • Fraternali F and Wipff G. A molecular dynamics study of complexation and stability of luminescent cations encapsulating ligands with bipyridine units. Phys. Org. Chem. 10 292–304 (1997).
  • Musco G, Kharrat A, Stier G, Fraternali F, Gibson TJ, Nilges M and Pastore A. The solution structure of the first KH domain of FMR1, the protein responsible for the fragile X syndrome. Struct. Biol. 4 712–716 (1997).
  • Ulrich G, Ziessel R, Manet I, Guardigli M, Sabbatini N, Fraternali F and Wipff G. Calix[4]arene in podants and barrelands incorporating 2-2’-bipyridinemoieties and their lanthanide complexes: luminescence properties. Eur. J. 3 1815–1822 (1997).
  • Fraternali F and Van Gunsteren WF. An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution. Mol. Biol. 256 939–948 (1996).
  • Benedetti E, Carlomagno T, Fraternali F, Hamada Y, Hayashi K, Paolillo L and Shioiri T. Conformational analysis of dolastatin 10: an NMR and theoretical approach. Biopolymers 36 525–538 (1995).
  • Fraternali F and Van Gunsteren WF. Conformational transitions of a dipeptide in water: effects of imposed pathways using umbrella sampling techniques. Biopolymers 34 347–355 (1994).
  • Paolillo L, D’Auria G, Falcigno L, Fraternali F, Saviano M, Simonetti M and Di Bello C. Conformational studies on peptide fragments related to ocytocin and somatostatin precursors. Top. in Pep. Prot. Res. 1 193–222 (1994).
  • Van Gunsteren WF, Beutler TC, Fraternali F, King PM, Mark AE and Smith PE. Computation of free energy in practice: choice of approximations and accuracy limiting factors. In Van Gunsteren WF, Weiner PK and Wilkinson AJ, editors, Computer simulation of biomolecular systems, theoretical and experimental applications, volume 2, 315–347. Escom Science Publishers BV (1993).
  • Pavone V, Lombardi A, Nastri F, Saviano M, Di Blasio B, Fraternali F, Pedone A and Yamada T. First observation of a helical peptide containing chiral ?-monosubstituted residues without a preferred screw sense. Chem. Soc. – Perkin Trans. II 971–977 (1992).
  • Crisma M, Valle G, Bonora GM, Toniolo C, Lelj F, Barone V, Fraternali F, Hardy PM and Maia HL. Preferred conformation of peptides from C?,?-symmetrically disubstituted glycines: aromatic residues. Biopolymers 31 637–641 (1991).
  • Toniolo C, Crisma M, Valle G, Bonora GM, Lelj F, Barone V, Fraternali F and Hardy HLS P M Maia. Conformational analysis of peptides from C?,?-symmetrically disubstituted aromatic -amino acid residues. In Giralt E and Andreu D, editors, Peptides, 458–459. Escom Science Publishers BV (1991).
  • Amodeo P, Barone V and Fraternali F. A microscopic approach to the structure and thermodynamic properties of peptides and proteins. Thermochimica Acta 162 141–154 (1990).
  • Barone V, Fraternali F and Cristinziano PL. Sensitivity of peptide conformation to methods and geometrical parameters. A comparative ab initio and molecular mechanics study of oligomers of -aminoisobutyric acid. Macromolecules 23 2038–2044 (1990).
  • Crisma M, Valle G, Bonora GM, De Menego E, Toniolo C, Lelj F, Barone V and Fraternali F. Linear oligopeptides 223. Structural versatility of peptides from C?,?-disubstituted glycines. Preferred conformation of the C?,?-diphenylglycine residue. Biopolymers 30 1–11 (1990).
  • Fraternali F. Restrained and unrestrained molecular dynamics simulations in the NVT ensemble of alamethicin. Biopolymers 30 1083–1099 (1990).
  • Valle G, Crisma M, Bonora GM, Toniolo C, Lelj F, Barone V, Fraternali F, Hardy PM and Langran-Goldsmith A. Structural versatility of peptides from C?,?-disubstituted glycines. Preferred conformation of the C?,?-dibenzylglycine residue. Chem. Soc. – Perkin Trans. II 1481–1487 (1990).
  • Zanotti G, Paolillo L, Barbato G, Fraternali F and D’Alagni M. Cation binding to heterodetic peptidic systems: CD and NMR structural studies. In Giralt E and Andreu D, editors, Peptides, 499–500. Escom Science Publishers BV (1990).
  • Benedetti E, Di Blasio B, Pavone V, Pedone C, Santini A, Barone V, Fraternali F, Lelj F, Bavoso A and Crisma M. Structural versatility of peptides containing C?,?-dialkylated glycines. An X-ray diffraction study of six 1-aminocyclopropane-carboxylic acid rich peptides. J. Biol. Macromol. 11 353–360 (1989).
  • Crisma M, Bonora GM, Toniolo C, Barone V, Benedetti E, Di Blasio B, Pavone V, Pedone C, Santini A and Fraternali F. Structural versatility of peptides containing C?,?-dialkylated glycines: conformational energy computations, IR absorption and 1H-NMR analysis of 1-aminocyclopropane-1-carboxylic acid homopeptides. J. Biol. Macromol. 11 345–352 (1989).
  • Barone V, Fraternali F, Cristinziano PL, Lelj F and Rosa A. Conformational behaviour of C?,?-dialkylated peptides: ab initio and empirical results for cyclopropylglycine. Biopolymers 27 1673–1685 (1988).
  • Santini A, Barone V, Bavoso A, Benedetti E, Di Blasio B, Fraternali F, Lelj F, Pavone V, Pedone C, Crisma M, Bonora GM and Toniolo C. Structural versatility of peptides from C?,?-dialkylated glycines: a conformational energy calculation and Xray diffraction study of homopeptides from 1-aminocyclopentane-1-carboxylic acid. J. Biol. Macromol. 10 292–299 (1988).
  • Toniolo C, Valle G, Bonora GM, Lelj F, Barone V, Fraternali F, Callet G, Wagnon J and Nisato D. Conformational preferences and self-association modes of two diastereomeric statine derivatives. J. Pept. Protein. Res. 30 583–595 (1987).