Abdullah Kahraman
Abdullah Kahraman
Head of Clinical Bioinformatics in Molecular Tumor Profiling, University Hospital Zurich
Verified email at usz.ch
TitleCited byYear
Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics
A Leitner, T Walzthoeni, A Kahraman, F Herzog, O Rinner, M Beck, ...
Molecular & Cellular Proteomics 9 (8), 1634-1649, 2010
4002010
Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry
F Herzog, A Kahraman, D Boehringer, R Mak, A Bracher, T Walzthoeni, ...
Science 337 (6100), 1348-1352, 2012
3222012
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
RJ Morris, RJ Najmanovich, A Kahraman, JM Thornton
Bioinformatics 21 (10), 2347-2355, 2005
2282005
Shape variation in protein binding pockets and their ligands
A Kahraman, RJ Morris, RA Laskowski, JM Thornton
Journal of molecular biology 368 (1), 283-301, 2007
2182007
Global analysis of protein structural changes in complex proteomes
Y Feng, G De Franceschi, A Kahraman, M Soste, A Melnik, PJ Boersema, ...
Nature biotechnology 32 (10), 1036, 2014
1192014
Distance restraints from crosslinking mass spectrometry: mining a molecular dynamics simulation database to evaluate lysine–lysine distances
ED Merkley, S Rysavy, A Kahraman, RP Hafen, V Daggett, JN Adkins
Protein science 23 (6), 747-759, 2014
1162014
Cross-link guided molecular modeling with ROSETTA
A Kahraman, F Herzog, A Leitner, G Rosenberger, R Aebersold, ...
PloS one 8 (9), e73411, 2013
1072013
Heme proteins—diversity in structural characteristics, function, and folding
LJ Smith, A Kahraman, JM Thornton
Proteins: structure, function, and bioinformatics 78 (10), 2349-2368, 2010
1072010
Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability
P Leuenberger, S Ganscha, A Kahraman, V Cappelletti, PJ Boersema, ...
Science 355 (6327), eaai7825, 2017
992017
Xwalk: computing and visualizing distances in cross-linking experiments
A Kahraman, L Malmström, R Aebersold
Bioinformatics 27 (15), 2163-2164, 2011
952011
PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics
A Kahraman, A Avramov, LG Nashev, D Popov, R Ternes, HD Pohlenz, ...
Bioinformatics 21 (3), 418-420, 2004
832004
Statistical methods for detecting differentially methylated loci and regions
MD Robinson, A Kahraman, CW Law, H Lindsay, M Nowicka, LM Weber, ...
Frontiers in genetics 5, 324, 2014
742014
xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints
M Grimm, T Zimniak, A Kahraman, F Herzog
Nucleic acids research 43 (W1), W362-W369, 2015
532015
On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins
A Kahraman, RJ Morris, RA Laskowski, AD Favia, JM Thornton
Proteins: Structure, Function, and Bioinformatics 78 (5), 1120-1136, 2010
502010
Proteomics beyond large-scale protein expression analysis
PJ Boersema, A Kahraman, P Picotti
Current opinion in biotechnology 34, 162-170, 2015
412015
Molecular details underlying dynamic structures and regulation of the human 26S proteasome
X Wang, P Cimermancic, C Yu, A Schweitzer, N Chopra, JL Engel, ...
Molecular & Cellular Proteomics 16 (5), 840-854, 2017
352017
Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry
S Schopper, A Kahraman, P Leuenberger, Y Feng, I Piazza, O Müller, ...
nature protocols 12 (11), 2391, 2017
212017
Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes
E Rheinbay, MM Nielsen, F Abascal, G Tiao, H Hornshøj, JM Hess, ...
bioRxiv, 237313, 2017
142017
Spin trapping combined with quantitative mass spectrometry defines free radical redistribution within the oxidized hemoglobin: haptoglobin complex
F Vallelian, I Garcia-Rubio, M Puglia, A Kahraman, JW Deuel, ...
Free Radical Biology and Medicine 85, 259-268, 2015
142015
The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases
SIB Swiss Institute of Bioinformatics Members
Nucleic acids research 44 (D1), D27-D37, 2015
132015
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