Claudia Andreini

Summary

Affiliation: University of Florence
Country: Italy

Publications

  1. pmc MetalPDB: a database of metal sites in biological macromolecular structures
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, Via L Sacconi 6, 50019 Sesto, Fiorentino, Italy
    Nucleic Acids Res 41:D312-9. 2013
  2. ncbi FindGeo: a tool for determining metal coordination geometry
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Italy
    Bioinformatics 28:1658-60. 2012
  3. pmc Predicting zinc binding at the proteome level
    Andrea Passerini
    Machine Learning and Neural Networks Group, Dipartimento di Sistemi e Informatica, Universita degli Studi di Firenze, Italy
    BMC Bioinformatics 8:39. 2007
  4. doi Metal-MACiE: a database of metals involved in biological catalysis
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino, Italy
    Bioinformatics 25:2088-9. 2009
  5. ncbi Metalloproteomes: a bioinformatic approach
    Claudia Andreini
    Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Italy
    Acc Chem Res 42:1471-9. 2009
  6. doi Structural analysis of metal sites in proteins: non-heme iron sites as a case study
    Claudia Andreini
    Magnetic Resonance Center CERM University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Italy
    J Mol Biol 388:356-80. 2009
  7. ncbi Occurrence of copper proteins through the three domains of life: a bioinformatic approach
    Claudia Andreini
    Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Italy
    J Proteome Res 7:209-16. 2008
  8. ncbi MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids
    Claudia Andreini
    Magnetic Resonance Center CERM University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
    J Chem Inf Model 53:3064-75. 2013
  9. ncbi Non-heme iron through the three domains of life
    Claudia Andreini
    Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
    Proteins 67:317-24. 2007
  10. doi Metal ions in biological catalysis: from enzyme databases to general principles
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, Via L Sacconi 6, 50019, Sesto Fiorentino, Italy
    J Biol Inorg Chem 13:1205-18. 2008

Collaborators

Detail Information

Publications20

  1. pmc MetalPDB: a database of metal sites in biological macromolecular structures
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, Via L Sacconi 6, 50019 Sesto, Fiorentino, Italy
    Nucleic Acids Res 41:D312-9. 2013
    ..MetalPDB is updated monthly in an automated manner...
  2. ncbi FindGeo: a tool for determining metal coordination geometry
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Italy
    Bioinformatics 28:1658-60. 2012
    ..FindGeo works by superimposing the metal-coordinating atoms in the input structure to a library of templates with alternative ideal geometries, which are ranked by RMSD to identify the best geometry assignment...
  3. pmc Predicting zinc binding at the proteome level
    Andrea Passerini
    Machine Learning and Neural Networks Group, Dipartimento di Sistemi e Informatica, Universita degli Studi di Firenze, Italy
    BMC Bioinformatics 8:39. 2007
    ..Metal-binding properties remain difficult to predict as well as to investigate experimentally at the whole-proteome level. Consequently, the current knowledge about metalloproteins is only partial...
  4. doi Metal-MACiE: a database of metals involved in biological catalysis
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino, Italy
    Bioinformatics 25:2088-9. 2009
    ..The two databases constitute complementary sources of information for enzymology, biochemistry and molecular pharmacology studies...
  5. ncbi Metalloproteomes: a bioinformatic approach
    Claudia Andreini
    Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Italy
    Acc Chem Res 42:1471-9. 2009
    ....
  6. doi Structural analysis of metal sites in proteins: non-heme iron sites as a case study
    Claudia Andreini
    Magnetic Resonance Center CERM University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Italy
    J Mol Biol 388:356-80. 2009
    ..Structural templates of metal sites, finally, may constitute the basis for a systematic classification of metalloproteins in databases...
  7. ncbi Occurrence of copper proteins through the three domains of life: a bioinformatic approach
    Claudia Andreini
    Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Italy
    J Proteome Res 7:209-16. 2008
    ..A network involving proteins having roles in both copper transport and respiration was identified, parts or all of which are detected in the majority of the organisms examined...
  8. ncbi MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids
    Claudia Andreini
    Magnetic Resonance Center CERM University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
    J Chem Inf Model 53:3064-75. 2013
    ..MetalS(2) supports the comparison of MFSs harboring different metals and/or with different nuclearity and is available both as a stand-alone program and a Web tool ( http://metalweb.cerm.unifi.it/tools/metals2/)...
  9. ncbi Non-heme iron through the three domains of life
    Claudia Andreini
    Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
    Proteins 67:317-24. 2007
    ..9% +/- 1.6%) and in eukaryota (1.1% +/- 0.4%). The analysis of the function of each putative iron-protein identified suggests that extant organisms have inherited the large majority of their iron-proteome from the last common ancestor...
  10. doi Metal ions in biological catalysis: from enzyme databases to general principles
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, Via L Sacconi 6, 50019, Sesto Fiorentino, Italy
    J Biol Inorg Chem 13:1205-18. 2008
    ..The control of the reactivity of redox-active metal ions may involve their association with organic cofactors to form stable units. This occurs sometimes for iron and nickel, and quite often for cobalt and molybdenum...
  11. ncbi Zinc through the three domains of life
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Italy
    J Proteome Res 5:3173-8. 2006
    ..8%) is significantly higher than that observed in Bacteria and Archaea (from 5% to 6%). Most of this enrichment is due to the larger portfolio of regulatory proteins in Eukaryota...
  12. ncbi Comparative analysis of the ADAM and ADAMTS families
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Italy
    J Proteome Res 4:881-8. 2005
    ....
  13. ncbi Counting the zinc-proteins encoded in the human genome
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Italy
    J Proteome Res 5:196-201. 2006
    ..The most abundant class of zinc-binding proteins in humans is that of zinc-fingers, with Cys4 and Cys2His2 being the most common types of coordination environment...
  14. ncbi A bioinformatics view of zinc enzymes
    Claudia Andreini
    Magnetic Resonance Center CERM University of Florence, Via L Sacconi 6, Sesto Fiorentino, Italy
    J Inorg Biochem 111:150-6. 2012
    ....
  15. pmc Minimal functional sites allow a classification of zinc sites in proteins
    Claudia Andreini
    Magnetic Resonance Center, University of Florence, Sesto Fiorentino, Italy
    PLoS ONE 6:e26325. 2011
    ....
  16. ncbi A hint to search for metalloproteins in gene banks
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, Italy
    Bioinformatics 20:1373-80. 2004
    ..Sometimes, metal binding can be observed in vitro but not be physiologically relevant. At present, there is a lack of specific tools to address the matter of the identification of metalloproteins in databases of gene sequences...
  17. doi A simple protocol for the comparative analysis of the structure and occurrence of biochemical pathways across superkingdoms
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, Sesto Fiorentino, Italy
    J Chem Inf Model 51:730-8. 2011
    ..As examples, we analyzed the pathways for the degradation of organic compounds containing one or two aromatic rings as well as the distribution of some proteins involved in Cu(A) assembly in more than a thousand prokaryotes...
  18. ncbi Bioinformatic comparison of structures and homology-models of matrix metalloproteinases
    Claudia Andreini
    Magnetic Resonance Center CERM, University of Florence, Via L Sacconi 6, 50019 Sesto Fiorentino, Italy
    J Proteome Res 3:21-31. 2004
    ....
  19. ncbi MetalS(3), a database-mining tool for the identification of structurally similar metal sites
    Yana Valasatava
    Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
    J Biol Inorg Chem 19:937-45. 2014
    ..Furthermore, we describe some usage scenarios that highlight the usefulness of MetalS(3) to obtain mechanistic and functional hints regardless of homology. ..
  20. pmc MACiE: exploring the diversity of biochemical reactions
    Gemma L Holliday
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D783-9. 2012
    ..We present new tools for exploring the data in MACiE and comparing entries as well as new analyses of the data and new searches, many of which can now be accessed via dedicated Perl scripts...