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Abdullah Kahraman
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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
5612010
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
5092020
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
4422012
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
3812017
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), 1036-1044, 2014
3482014
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
2862014
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
2692007
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
2652005
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), 2391-2410, 2017
2042017
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
1882010
Cross-link guided molecular modeling with ROSETTA
A Kahraman, F Herzog, A Leitner, G Rosenberger, R Aebersold, ...
PloS one 8 (9), e73411, 2013
1752013
Xwalk: computing and visualizing distances in cross-linking experiments
A Kahraman, L Malmström, R Aebersold
Bioinformatics 27 (15), 2163-2164, 2011
1612011
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
1352014
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
1302015
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
1022017
Pathway and network analysis of more than 2500 whole cancer genomes
MA Reyna, D Haan, M Paczkowska, LPC Verbeke, M Vazquez, ...
Nature communications 11 (1), 729, 2020
942020
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
932005
The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support
A Irmisch, X Bonilla, S Chevrier, KV Lehmann, F Singer, NC Toussaint, ...
Cancer Cell 39 (3), 288-293, 2021
892021
Proteomics beyond large-scale protein expression analysis
PJ Boersema, A Kahraman, P Picotti
Current opinion in biotechnology 34, 162-170, 2015
732015
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
672010
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