Abdullah Kahraman
Abdullah Kahraman
Head of Clinical Bioinformatics in Molecular Tumor Profiling, University Hospital Zurich
Verified email at usz.ch
Title
Cited by
Cited by
Year
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
4372010
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
3482012
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
2302005
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
2232007
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
1392014
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
1382014
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
1272017
Cross-link guided molecular modeling with ROSETTA
A Kahraman, F Herzog, A Leitner, G Rosenberger, R Aebersold, ...
PloS one 8 (9), 2013
1222013
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
1122010
Xwalk: computing and visualizing distances in cross-linking experiments
A Kahraman, L Malmström, R Aebersold
Bioinformatics 27 (15), 2163-2164, 2011
1092011
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, 2005
842005
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
802014
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
652015
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
532010
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
482017
Proteomics beyond large-scale protein expression analysis
PJ Boersema, A Kahraman, P Picotti
Current opinion in biotechnology 34, 162-170, 2015
472015
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
342017
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
252017
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
E Rheinbay, MM Nielsen, F Abascal, JA Wala, O Shapira, G Tiao, ...
Nature 578 (7793), 102-111, 2020
192020
The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases
SIB Swiss Institute of Bioinformatics Members
Nucleic acids research 44 (D1), D27-D37, 2016
172016
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Articles 1–20