Abdullah Kahraman

Summary

Affiliation: Swiss Federal Institute of Technology
Country: Switzerland

Publications

  1. doi request reprint On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins
    Abdullah Kahraman
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
    Proteins 78:1120-36. 2010
  2. pmc Xwalk: computing and visualizing distances in cross-linking experiments
    Abdullah Kahraman
    Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology ETH Zurich, CH 8093 Zurich, Switzerland
    Bioinformatics 27:2163-4. 2011
  3. ncbi request reprint Shape variation in protein binding pockets and their ligands
    Abdullah Kahraman
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
    J Mol Biol 368:283-301. 2007
  4. ncbi request reprint Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
    Richard J Morris
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 21:2347-55. 2005
  5. doi request reprint Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry
    Franz Herzog
    Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Science 337:1348-52. 2012
  6. pmc Cross-link guided molecular modeling with ROSETTA
    Abdullah Kahraman
    Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, Zurich, Switzerland
    PLoS ONE 8:e73411. 2013
  7. pmc Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics
    Alexander Leitner
    Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule ETH Zurich, Zurich, Switzerland
    Mol Cell Proteomics 9:1634-49. 2010

Collaborators

Detail Information

Publications7

  1. doi request reprint On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins
    Abdullah Kahraman
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
    Proteins 78:1120-36. 2010
    ..The presented results highlight the complexities of molecular recognition and underline the challenges of computational structural biology in developing methods to detect these important subtleties...
  2. pmc Xwalk: computing and visualizing distances in cross-linking experiments
    Abdullah Kahraman
    Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology ETH Zurich, CH 8093 Zurich, Switzerland
    Bioinformatics 27:2163-4. 2011
    ..Chemical cross-linking of proteins or protein complexes and the mass spectrometry-based localization of the cross-linked amino acids in peptide sequences is a powerful method for generating distance restraints on the substrate's topology...
  3. ncbi request reprint Shape variation in protein binding pockets and their ligands
    Abdullah Kahraman
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
    J Mol Biol 368:283-301. 2007
    ..Additionally, we observe a "buffer zone" or a region of free space between the ligand and protein, which results in binding pockets being on average three times larger than the ligand that they bind...
  4. ncbi request reprint Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
    Richard J Morris
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 21:2347-55. 2005
    ....
  5. doi request reprint Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry
    Franz Herzog
    Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Science 337:1348-52. 2012
    ..This study establishes XL-MS as an integral part of hybrid structural biology approaches for the analysis of endogenous protein complexes...
  6. pmc Cross-link guided molecular modeling with ROSETTA
    Abdullah Kahraman
    Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, Zurich, Switzerland
    PLoS ONE 8:e73411. 2013
    ....
  7. pmc Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics
    Alexander Leitner
    Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule ETH Zurich, Zurich, Switzerland
    Mol Cell Proteomics 9:1634-49. 2010
    ..Finally, the impact of protein cross-linking on various biological disciplines is highlighted...