Affiliation: Swiss Federal Institute of Technology
- On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteinsAbdullah 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...
- Xwalk: computing and visualizing distances in cross-linking experimentsAbdullah 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...
- Shape variation in protein binding pockets and their ligandsAbdullah 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...
- Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisonsRichard J Morris
EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Bioinformatics 21:2347-55. 2005....
- Cross-link guided molecular modeling with ROSETTAAbdullah Kahraman
Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, Zurich, Switzerland
PLoS ONE 8:e73411. 2013....
- Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometryFranz 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...
- Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformaticsAlexander 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...