Marcin Feder

Summary

Affiliation: International Institute of Molecular and Cell Biology
Country: Poland

Publications

  1. pmc Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily
    Elena M Ibryashkina
    Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
    BMC Struct Biol 7:48. 2007
  2. ncbi request reprint Virtual screening and experimental verification to identify potential inhibitors of the ErmC methyltransferase responsible for bacterial resistance against macrolide antibiotics
    Marcin Feder
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02109 Warsaw, Poland
    ChemMedChem 3:316-22. 2008
  3. pmc Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site
    Marcin Feder
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    BMC Genomics 6:21. 2005
  4. ncbi request reprint FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6
    Jan Kosinski
    International Institute of Molecular and Cell Biology, Warsaw, Poland
    Proteins 61:106-13. 2005
  5. ncbi request reprint Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis
    Elzbieta Purta
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
    Proteins 59:482-8. 2005
  6. ncbi request reprint Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases
    Marcin Feder
    Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, ul ks Trojdena 4, 02 109, Warsaw, Poland
    Gene 302:129-38. 2003
  7. pmc Phylogenomic analysis of the GIY-YIG nuclease superfamily
    Stanislaw Dunin-Horkawicz
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    BMC Genomics 7:98. 2006
  8. ncbi request reprint A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation
    Jan Kosinski
    Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    Proteins 53:369-79. 2003
  9. pmc Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases
    Janusz M Bujnicki
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
    Nucleic Acids Res 32:2453-63. 2004
  10. pmc The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
    Jan Kosinski
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL 02 109 Warsaw, Poland
    BMC Bioinformatics 6:172. 2005

Collaborators

Detail Information

Publications20

  1. pmc Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily
    Elena M Ibryashkina
    Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
    BMC Struct Biol 7:48. 2007
    ..The determination of a crystal structure of the GIY-YIG domain of homing endonuclease I-TevI provided a template for modeling of R.Eco29kI and prompted us to validate the model experimentally...
  2. ncbi request reprint Virtual screening and experimental verification to identify potential inhibitors of the ErmC methyltransferase responsible for bacterial resistance against macrolide antibiotics
    Marcin Feder
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02109 Warsaw, Poland
    ChemMedChem 3:316-22. 2008
    ..Eight of them have IC(50) values in the micromolar range. Analysis of docking models of the identified inhibitors suggests a novel strategy to develop potent and clinically useful inhibitors...
  3. pmc Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site
    Marcin Feder
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    BMC Genomics 6:21. 2005
    ..Here, we predict the three-dimensional fold and study the phylogenomic distribution of members of a large family of uncharacterized proteins classified in the Clusters of Orthologous Groups database as COG4636...
  4. ncbi request reprint FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6
    Jan Kosinski
    International Institute of Molecular and Cell Biology, Warsaw, Poland
    Proteins 61:106-13. 2005
    ....
  5. ncbi request reprint Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis
    Elzbieta Purta
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
    Proteins 59:482-8. 2005
    ....
  6. ncbi request reprint Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases
    Marcin Feder
    Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, ul ks Trojdena 4, 02 109, Warsaw, Poland
    Gene 302:129-38. 2003
    ..The results of our analysis of phylogenetic relationships in the RrmJ/fibrillarin superfamily provide insight into the evolution of site-specific and snoRNA-guided ribose 2'-O-MTases from a common ancestor...
  7. pmc Phylogenomic analysis of the GIY-YIG nuclease superfamily
    Stanislaw Dunin-Horkawicz
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    BMC Genomics 7:98. 2006
    ..However, to date no systematic search for novel members of the GIY-YIG superfamily or comparative analysis of these enzymes has been reported...
  8. ncbi request reprint A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation
    Jan Kosinski
    Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    Proteins 53:369-79. 2003
    ..The automatic version of our multi-step protocol is being developed as a meta-server; the prototype is freely available at http://genesilico.pl/meta/...
  9. pmc Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases
    Janusz M Bujnicki
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
    Nucleic Acids Res 32:2453-63. 2004
    ....
  10. pmc The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
    Jan Kosinski
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL 02 109 Warsaw, Poland
    BMC Bioinformatics 6:172. 2005
    ..Thus, it is tempting to speculate that among the uncharacterized protein families, there are potential nucleases that remain to be discovered, but their identification requires more sensitive tools than traditional PSI-BLAST searches...
  11. pmc Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures
    Michal A Kurowski
    Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    BMC Bioinformatics 4:9. 2003
    ....
  12. pmc MODOMICS: a database of RNA modification pathways
    Stanislaw Dunin-Horkawicz
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul ks Trojdena 4, PL 02 190 Warsaw, Poland
    Nucleic Acids Res 34:D145-9. 2006
    ..The contents of MODOMICS can be accessed through the World Wide Web at http://genesilico.pl/modomics/...
  13. ncbi request reprint Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA:m(6)A methyltransferase
    Janusz M Bujnicki
    Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, ul ks Trojdena 4, 02 109 Warsaw, Poland
    J Mol Evol 55:431-44. 2002
    ..Significantly, this consensus fold shows the permuted topology characteristic of the b class of MTases, which to date has only been known to include DNA MTases...
  14. pmc Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA
    Agnieszka Obarska
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    Nucleic Acids Res 34:1992-2005. 2006
    ..The model structure, together with location of the mutant residues, provides a better background on which to study protein-protein and protein-DNA interactions in Type I R-M systems...
  15. ncbi request reprint Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'
    Gordana Maravić
    Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012 Trieste, Italy
    J Mol Biol 332:99-109. 2003
    ..This somewhat surprising result is discussed in the light of the available structural data and in the phylogenetic context of the Erm family...
  16. ncbi request reprint Identification of a missing sequence and functionally important residues of 16S rRNA:m(1)A1408 methyltransferase KamB that causes bacterial resistance to aminoglycoside antibiotics
    Lukasz Koscinski
    Cell Cycle 6:1268-71. 2007
  17. ncbi request reprint Errors in the D. radiodurans large ribosomal subunit structure detected by protein fold-recognition and structure validation tools
    Janusz M Bujnicki
    FEBS Lett 525:174-5. 2002
  18. pmc Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions
    Gordana Maravić
    Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology ICGEB, Padriciano 99, 34012 Trieste, Italy
    Nucleic Acids Res 31:4941-9. 2003
    ....
  19. ncbi request reprint Characterization of prmt7alpha and beta isozymes from Chinese hamster cells sensitive and resistant to topoisomerase II inhibitors
    Laurent Gros
    CNRS FRE2618, Laboratoire de Pharmacologie des Agents Anticancéreux, Institut Bergonie, 229 Cours de l Argonne, 33076 Bordeaux, France
    Biochim Biophys Acta 1760:1646-56. 2006
    ..Analysis of in vitro and in vivo methylation patterns in cell lines under- or over-expressing PRMT7alpha and beta detected a discrete number of proteins which methylation and/or expression are under the control of these enzymes...
  20. pmc Complete cap 4 formation is not required for viability in Trypanosoma brucei
    Jesse R Zamudio
    Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095 1489, USA
    Eukaryot Cell 5:905-15. 2006
    ..As mature cap 4 is dispensable for translation, cap 1 modifications and/or SL sequences are implicated in ribosomal interaction...