| Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2 Z Kurkcuoglu, PI Koukos, N Citro, ME Trellet, J Rodrigues, IS Moreira, ... Journal of computer-aided molecular design 32 (1), 175-185, 2018 | 155 | 2018 |
| INDIGO-DataCloud: A data and computing platform to facilitate seamless access to e-infrastructures D Salomoni, I Campos, L Gaido, JM de Lucas, P Solagna, J Gomes, ... arXiv preprint arXiv:1711.01981, 2017 | 77 | 2017 |
| Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1 A Vangone, JPGLM Rodrigues, LC Xue, GCP van Zundert, C Geng, ... Proteins: Structure, Function, and Bioinformatics, 2016 | 76 | 2016 |
| The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes GCP van Zundert, M Trellet, J Schaarschmidt, Z Kurkcuoglu, M David, ... Journal of Molecular Biology 429 (3), 399–407, 2017 | 67 | 2017 |
| Coupling between Catalytic Loop Motions and Enzyme Global Dynamics Z Kurkcuoglu, A Bakan, D Kocaman, I Bahar, P Doruker PLOS Computational Biology 8 (9), e1002705, 2012 | 64 | 2012 |
| ClustENM: ENM-based sampling of essential conformational space at full atomic resolution Z Kurkcuoglu, I Bahar, P Doruker Journal of chemical theory and computation 12 (9), 4549-4562, 2016 | 60 | 2016 |
| Collective dynamics of the ribosomal tunnel revealed by elastic network modeling O Kurkcuoglu, Z Kurkcuoglu, P Doruker, RL Jernigan Proteins: Structure, Function, and Bioinformatics 75 (4), 837-845, 2009 | 53 | 2009 |
| Pre‐and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems Z Kurkcuoglu, AMJJ Bonvin Proteins: Structure, Function, and Bioinformatics 88 (2), 292-306, 2020 | 43 | 2020 |
| How an inhibitor bound to subunit interface alters triosephosphate isomerase dynamics Z Kurkcuoglu, D Findik, ED Akten, P Doruker Biophysical Journal 109 (6), 1169-1178, 2015 | 34 | 2015 |
| Ligand docking to intermediate and close-to-bound conformers generated by an elastic network model based algorithm for highly flexible proteins Z Kurkcuoglu, P Doruker PloS one 11 (6), e0158063, 2016 | 31 | 2016 |
| An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45 PI Koukos, J Roel‐Touris, F Ambrosetti, C Geng, J Schaarschmidt, ... Proteins: Structure, Function, and Bioinformatics 88 (8), 1029-1036, 2020 | 19 | 2020 |
| Understanding the binding specificity of G-protein coupled receptors toward G-proteins and arrestins: application to the dopamine receptor family AJ Preto, CAV Barreto, SJ Baptista, JG Almeida, A Lemos, A Melo, ... Journal of Chemical Information and Modeling 60 (8), 3969-3984, 2020 | 17 | 2020 |
| Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human Z Kurkcuoglu, G Ural, E Demet Akten, P Doruker Molecular informatics 30 (11‐12), 986-995, 2011 | 15 | 2011 |
| Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states MT Can, Z Kurkcuoglu, G Ezeroglu, A Uyar, O Kurkcuoglu, P Doruker PLoS One 12 (4), e0176262, 2017 | 10 | 2017 |
| Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase Z Kurkcuoglu, P Doruker Entropy 15 (3), 1085-1099, 2013 | 6 | 2013 |
| Sense and simplicity in HADDOCK scoring: lessons from CASP‐CAPRI (page 418) A Vangone, J Rodrigues, LC Xue, GCP van Zundert, C Geng, ... Proteins: Structure, Function, and Bioinformatics 85 (8), 1589-1590, 2017 | 5 | 2017 |
| HADDOCK AMJJ Bonvin, C Geng, M van Dijk, E Karaca, PL Kastritis, PI Koukos, ... Encyclopedia of Biophysics, 1-3, 2018 | 2* | 2018 |
| Functional Dynamics of Proteins Elucidated by Statistical Analysis of Simulation Data B Alakent, Z Kurkcuoglu, P Doruker Current Physical Chemistry 2 (4), 443-451, 2012 | 1 | 2012 |
| Real‐World Evidence BRIDGE: A Tool to Connect Protocol With Code Programming AC Royo, R Elbers Jhj, D Weibel, V Hoxhaj, Z Kurkcuoglu, ... Pharmacoepidemiology and Drug Safety 33 (12), e70062, 2024 | | 2024 |
| Real-World Evidence BRIDGE: a tool to connect protocol with code programming R Elbers, D Weibel, V Hoxhaj, Z Kurkcuoglu, M Sturkenboom, TA Vaz, ... | | 2024 |
Pemra DorukerUniversity of Pittsburgh, Bogazici UniversityVerified email at pitt.edu
