Jan Kosinski

Summary

Affiliation: University of Rome La Sapienza
Country: Italy

Publications

  1. pmc Improving your target-template alignment with MODalign
    Alessandro Barbato
    Department of Physics, Sapienza University P le A Moro, 5, 00185 Rome, Italy
    Bioinformatics 28:1038-9. 2012
  2. pmc Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair
    Jan Kosinski
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
    Hum Mutat 31:975-82. 2010
  3. doi request reprint The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family
    Jan Kosinski
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    J Mol Biol 382:610-27. 2008
  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 Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis
    Krzysztof J Skowronek
    International Institute of Molecular and Cell Biology, Warsaw, Poland
    Proteins 63:1059-68. 2006
  6. ncbi request reprint A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering
    Jan Kosinski
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    Proteins 68:324-36. 2007
  7. pmc REPAIRtoire--a database of DNA repair pathways
    Kaja Milanowska
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul ks Trojdena 4, 02 109 Warsaw, Poland
    Nucleic Acids Res 39:D788-92. 2011
  8. 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
  9. 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

Collaborators

Detail Information

Publications9

  1. pmc Improving your target-template alignment with MODalign
    Alessandro Barbato
    Department of Physics, Sapienza University P le A Moro, 5, 00185 Rome, Italy
    Bioinformatics 28:1038-9. 2012
    ..Although it has been designed to simplify the target-template alignment step in modeling, it is suitable for all cases where a sequence alignment needs to be inspected in the context of other biological information...
  2. pmc Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair
    Jan Kosinski
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
    Hum Mutat 31:975-82. 2010
    ..Ala586Pro, p.Leu636Pro, p.Thr662Pro, and p.Arg755Trp) are deleterious because of poor expression or poor repair efficiency, and confirm the deleterious effect of eight further alterations...
  3. doi request reprint The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family
    Jan Kosinski
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    J Mol Biol 382:610-27. 2008
    ..Finally, we demonstrate that the conserved residues of the metal ion binding domain are crucial for MMR activity of MutLalpha in vitro...
  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 Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis
    Krzysztof J Skowronek
    International Institute of Molecular and Cell Biology, Warsaw, Poland
    Proteins 63:1059-68. 2006
    ....
  6. ncbi request reprint A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering
    Jan Kosinski
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02 109 Warsaw, Poland
    Proteins 68:324-36. 2007
    ..The model is in good agreement with the available experimental data and will serve as a template for further analyses of R.MvaI, R.BcnI, R.ScrFI and other related enzymes...
  7. pmc REPAIRtoire--a database of DNA repair pathways
    Kaja Milanowska
    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul ks Trojdena 4, 02 109 Warsaw, Poland
    Nucleic Acids Res 39:D788-92. 2011
    ..In addition, a tool for drawing custom DNA-protein complexes is available online. REPAIRtoire is freely available and can be accessed at http://repairtoire.genesilico.pl/...
  8. 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...
  9. 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/...