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Publication Restricted A comparative molecular dynamics study of HLA-B51 and HLA-B52: Implications for the pathogenic role of HLA-B51 in Behçet's disease(Koç University, 2014) Aydın, Deniz; Erman, Burak; 0000-0002-2496-6059; Koç University Graduate School of Sciences and Engineering; Chemical and Biological Engineering; 179997Publication Restricted A transferable coarse-grained model for peptides that display an environment driven conformational transition(Koç University, 2015) Ramezanghorbani, Farhad; Sayar, Mehmet; 0000-0003-0553-0353; Koç University Graduate School of Sciences and Engineering; Computational Sciences and Engineering; 109820
Publication Metadata only Candidate protein biomarkers in chronic kidney disease: a proteomics study(Nature Research, 2024) Makhammajanov, Zhalaliddin; Kabayeva, Assem; Auganova, Dana; Tarlykov, Pavel; Bukasov, Rostislav; Turebekov, Duman; Molnar, Miklos Z.; Kovesdy, Csaba P.; Abidi, Syed Hani; Gaipov, Abduzhappar; Kanbay, Mehmet; School of MedicineProteinuria poses a substantial risk for the progression of chronic kidney disease (CKD) and its related complications. Kidneys excrete hundreds of individual proteins, some with a potential impact on CKD progression or as a marker of the disease. However, the available data on specific urinary proteins and their relationship with CKD severity remain limited. Therefore, we aimed to investigate the urinary proteome and its association with kidney function in CKD patients and healthy controls. The proteomic analysis of urine samples showed CKD stage-specific differences in the number of detected proteins and the exponentially modified protein abundance index for total protein (p = 0.007). Notably, specific urinary proteins such as B2MG, FETUA, VTDB, and AMBP exhibited robust negative associations with kidney function in CKD patients compared to controls. Also, A1AG2, CD44, CD59, CERU, KNG1, LV39, OSTP, RNAS1, SH3L3, and UROM proteins showed positive associations with kidney function in the entire cohort, while LV39, A1BG, and CERU consistently displayed positive associations in patients compared to controls. This study suggests that specific urinary proteins, which were found to be negatively or positively associated with the kidney function of CKD patients, can serve as markers of dysfunctional or functional kidneys, respectively. © The Author(s) 2024.Publication Restricted Computational design of a pentapeptide inhibitor for fibroblast growth factor receptor (FGFR3) IIIB(Koç University, 2011) Öztürk, Mehmet Ali; Erman, Burak; 0000-0002-2496-6059; Koç University Graduate School of Sciences and Engineering; Computational Sciences and Engineering; 179997Publication Restricted Computational design of a peptide inhibitor for amyloid beta (A?) aggregation in alzheimer's disease(Koç University, 2010) Eskici, Gözde; Erman, Burak; 0000-0002-2496-6059; Koç University Graduate School of Sciences and Engineering; Computational Sciences and Engineering; 179997Publication Restricted Conformation of peptides in the unfolded state: a coarse-grained model representation(Koç University, 2007) Engin, Özge; Erman, Burak; Sayar, Mehmet; 0000-0002-2496-6059; 0000-0003-0553-0353; Koç University Graduate School of Sciences and Engineering; Computational Sciences and Engineering; 179997; 109820Publication Restricted De novo peptide design strategies(Koç University, 2011) Ünal, Evrim Besray; Erman, Burak; Gürsoy, Attila; 0000-0002-2496-6059; 0000-0002-2297-2113; Koç University Graduate School of Sciences and Engineering; Computational Sciences and Engineering; 179997; 8745Publication Restricted Environment induced conformational transition in peptides(Koç University, 2014) Dalgıçdır, Cahit; Sayar, Mehmet; 0000-0003-0553-0353; Koç University Graduate School of Sciences and Engineering; Computational Sciences and Engineering; 109820Publication Restricted Feminist lawyers in İstanbul : Re-thinking the boundaries between the legal and the non-legal(Koç University, 2016) Pınar, Fulya; Sayar, Mehmet; 0000-0003-0553-0353; Koç University Graduate School of Social Sciences and Humanities; Comparative Studies in History and Society; 109820Publication Restricted Human growth factor production towards in vitro vascularization(Koç University, 2022) Tunalı, Beste; Albayrak, Cem; 0000-0002-4496-4237; Koç University Graduate School of Sciences and Engineering; Chemical and Biological Engineering