Allegra Via

Summary

Affiliation: University of Rome La Sapienza
Country: Italy

Publications

  1. pmc Best practices in bioinformatics training for life scientists
    Allegra Via
    Department of Physics, Sapienza University, P le Aldo Moro 5, 00185 Rome, Italy
    Brief Bioinform 14:528-37. 2013
  2. pmc Artemether resistance in vitro is linked to mutations in PfATP6 that also interact with mutations in PfMDR1 in travellers returning with Plasmodium falciparum infections
    Dylan R Pillai
    Centre for Infection and Immunity, Division of Clinical Sciences, St, George S, University of London, London SW17 0RE, UK
    Malar J 11:131. 2012
  3. pmc Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract
    Emiliano Mancini
    Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Universita di Roma, Italy
    BMC Evol Biol 11:72. 2011
  4. pmc A structure filter for the Eukaryotic Linear Motif Resource
    Allegra Via
    Center for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy
    BMC Bioinformatics 10:351. 2009
  5. pmc 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures
    Allegra Via
    Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
    Nucleic Acids Res 35:W416-9. 2007
  6. pmc SH3-Hunter: discovery of SH3 domain interaction sites in proteins
    Enrico Ferraro
    Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
    Nucleic Acids Res 35:W451-4. 2007
  7. pmc FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures
    Gabriele Ausiello
    Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy
    BMC Bioinformatics 9:S2. 2008
  8. pmc Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites
    Gabriele Ausiello
    Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy
    BMC Bioinformatics 8:S24. 2007
  9. pmc Query3d: a new method for high-throughput analysis of functional residues in protein structures
    Gabriele Ausiello
    Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
    BMC Bioinformatics 6:S5. 2005
  10. pmc A neural strategy for the inference of SH3 domain-peptide interaction specificity
    Enrico Ferraro
    Centre for Molecular Bioinformatics, Department of Biology, University of Tor Vergata, Rome, Italy
    BMC Bioinformatics 6:S13. 2005

Collaborators

Detail Information

Publications20

  1. pmc Best practices in bioinformatics training for life scientists
    Allegra Via
    Department of Physics, Sapienza University, P le Aldo Moro 5, 00185 Rome, Italy
    Brief Bioinform 14:528-37. 2013
    ..Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists. ..
  2. pmc Artemether resistance in vitro is linked to mutations in PfATP6 that also interact with mutations in PfMDR1 in travellers returning with Plasmodium falciparum infections
    Dylan R Pillai
    Centre for Infection and Immunity, Division of Clinical Sciences, St, George S, University of London, London SW17 0RE, UK
    Malar J 11:131. 2012
    ..Monitoring resistance phenotypes for Plasmodium falciparum, using in vitro growth assays, and relating findings to parasite genotype has proved particularly challenging for the study of resistance to artemisinins...
  3. pmc Molecular evolution of a gene cluster of serine proteases expressed in the Anopheles gambiae female reproductive tract
    Emiliano Mancini
    Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Universita di Roma, Italy
    BMC Evol Biol 11:72. 2011
    ..gambiae females...
  4. pmc A structure filter for the Eukaryotic Linear Motif Resource
    Allegra Via
    Center for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy
    BMC Bioinformatics 10:351. 2009
    ..Several tools now use these attributes to classify putative motifs based on confidence of functionality...
  5. pmc 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures
    Allegra Via
    Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
    Nucleic Acids Res 35:W416-9. 2007
    ..The 3dLOGO server, with related documentation, is available at http://3dlogo.uniroma2.it/..
  6. pmc SH3-Hunter: discovery of SH3 domain interaction sites in proteins
    Enrico Ferraro
    Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
    Nucleic Acids Res 35:W451-4. 2007
    ..The server prediction capability is based on a neural network model integrating high-throughput pep-spot data with structural information extracted from known SH3-peptide complexes...
  7. pmc FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures
    Gabriele Ausiello
    Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy
    BMC Bioinformatics 9:S2. 2008
    ....
  8. pmc Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites
    Gabriele Ausiello
    Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy
    BMC Bioinformatics 8:S24. 2007
    ..With the purpose of finding new examples of convergent evolution, we selected only those matching sites composed of structural regions whose residue order is inverted in the relative protein sequences...
  9. pmc Query3d: a new method for high-throughput analysis of functional residues in protein structures
    Gabriele Ausiello
    Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
    BMC Bioinformatics 6:S5. 2005
    ....
  10. pmc A neural strategy for the inference of SH3 domain-peptide interaction specificity
    Enrico Ferraro
    Centre for Molecular Bioinformatics, Department of Biology, University of Tor Vergata, Rome, Italy
    BMC Bioinformatics 6:S13. 2005
    ..In this regard, a reliable inference methodology to be used for reducing the sequence space of putative binding peptides represents a valuable support for molecular and cellular biologists...
  11. doi request reprint Investigation of a potential mechanism for the inhibition of SmTGR by Auranofin and its implications for Plasmodium falciparum inhibition
    Antonia Caroli
    Department of Physics, Sapienza University of Rome, Rome, Italy
    Biochem Biophys Res Commun 417:576-81. 2012
    ..Our findings support a recently hypothesized molecular mechanism of inhibition for SmTGR and suggest that PfTR is indeed a possible and attractive drug target in P. falciparum...
  12. pmc pdbFun: mass selection and fast comparison of annotated PDB residues
    Gabriele Ausiello
    Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata via della Ricerca Scientifica, 00133 Rome, Italy
    Nucleic Acids Res 33:W133-7. 2005
    ..Possible examples of targets are represented by another selection, a single structure or a dataset composed of many structures. The output is a list of aligned structural matches offered in tabular and also graphical format...
  13. doi request reprint Identification of the Schistosoma mansoni molecular target for the antimalarial drug artemether
    Rosalba Lepore
    Department of Physics, Sapienza University of Rome, Rome, Italy
    J Chem Inf Model 51:3005-16. 2011
    ..Our analysis of the mode of binding of artemether to Ca²⁺-ATPases also provides an explanation for the apparent paradox that, although the molecule has no side effect in humans, it has been shown to possess antitumoral activity...
  14. pmc False occurrences of functional motifs in protein sequences highlight evolutionary constraints
    Allegra Via
    Centro di Bioinformatica Molecolare, Department of Biology, University of Rome Tor Vergata, Roma
    BMC Bioinformatics 8:68. 2007
    ..questions such as: How are organisms protected from undesirable occurrences of motifs otherwise selected for their functionality? Has the random appearance of functional motifs in protein sequences been affected during evolution?..
  15. pmc Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs
    Ahmed Sayadi
    Department of Physics, Sapienza University of Rome, Rome, Italy
    PLoS ONE 6:e22270. 2011
    ..biocomputing.it/modipath)...
  16. pmc A structural study for the optimisation of functional motifs encoded in protein sequences
    Allegra Via
    Centre for Molecular Bioinformatics, Dept, of Biology, University of Rome Tor Vergata, Rome, Italy
    BMC Bioinformatics 5:50. 2004
    ..If residues structurally conserved in proteins sharing a function cannot be aligned in a multiple sequence alignment, they are likely to be missed in a standard pattern construction procedure...
  17. pmc On the mechanism of chloroquine resistance in Plasmodium falciparum
    Mauro Chinappi
    Department of Biochemical Sciences, Sapienza University, Rome, Italy
    PLoS ONE 5:e14064. 2010
    ....
  18. ncbi request reprint Seq2Struct: a resource for establishing sequence-structure links
    Allegra Via
    Department of Biology, Centre for Molecular Bioinformatics, University of Rome Tor Vergata 00133 Rome, Italy
    Bioinformatics 21:551-3. 2005
    ..The Seq2Struct database contents, supported by a WWW web interface, can be queried both online and downloaded...
  19. pmc TiPs: a database of therapeutic targets in pathogens and associated tools
    Rosalba Lepore
    Department of Physics, Sapienza University, 00185 Rome, Italy
    Bioinformatics 29:1821-2. 2013
    ..Availability and implementation: The TiPs database is freely available at http://biocomputing.it/tips...
  20. ncbi request reprint From sequence to structural analysis in protein phosphorylation motifs
    Allegra Via
    Biocomputing Group, Department of Biochemical Science A Rossi Fanelli, Sapienza University of Rome, P le Aldo Moro 5, Rome, Italy
    Front Biosci (Landmark Ed) 16:1261-75. 2011
    ....