İSTE Yazarı "Rifaioğlu, Ahmet Süreyya" Makale Koleksiyonu İçin Listeleme
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CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations
Doğan, Tunca; Ataş, Heval; Joshi, Vishal; Atakan, Ahmet; Rifaioğlu, Ahmet Süreyya; Nalbat, Esra; Nightingale, Andrew; Saidi, Rabie; Volynkin, Vladimir; Zellner, Hermann; Atalay, Rengül Çetin; Martin, Maria; Atalay, Volkan (Oxford Academic, 2021)Systemic analysis of available large-scale biological/biomedical data is critical for studying biological mechanisms, and developing novel and effective treatment approaches against diseases. However, different layers of ... -
iBioProVis: interactive visualization and analysis of compound bioactivity space
Dönmez, Ataberk; Rifaioğlu, Ahmet Süreyya; Acar, Aybar; Doğan, Tunca; Atalay, Rengül Çetin; Atalay, Volkan (NLM (Medline), 2020)iBioProVis is an interactive tool for visual analysis of the compound bioactivity space in the context of target proteins, drugs and drug candidate compounds. iBioProVis tool takes target protein identifiers and, optionally, ... -
MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery
Rifaioğlu, Ahmet Süreyya; Atalay, R. Çetin; Kahraman, Deniz Cansen; Doğan, Tunca; Martín, María Jesús; Atalay, Volkan (Oxford University Press, 2021)Motivation: Identification of interactions between bioactive small molecules and target proteins is crucial for novel drug discovery, drug repurposing and uncovering off-target effects. Due to the tremendous size of the ... -
Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl
Karakulak, Tülay; Rifaioğlu, Ahmet Süreyya; Rodrigues, Joao P. G. L. M.; Karaca, Ezgi (Frontiers Media S.A., 2021)Owing to its clinical significance, modulation of functionally relevant amino acids in protein-protein complexes has attracted a great deal of attention. To this end, many approaches have been proposed to predict the ... -
ProFAB—open protein functional annotation benchmark
Özdilek, A. Samet; Atakan, Ahmet; Özsarı, Gökhan; Acar, Aybar; Atalay, M. Volkan; Doğan, Tunca; Rifaioğlu, Ahmet Süreyya (Oxford University Press, 2023)As the number of protein sequences increases in biological databases, computational methods are required to provide accurate functional annotation with high coverage. Although several machine learning methods have been ... -
SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins
Özsarı, Gökhan; Rifaioğlu, Ahmet Süreyya; Atakan, Ahmet; Tunca, Doğan; Martin, Maria Jesus; Atalay, Rengül Çetin; Atalay, Volkan (Oxford University Press, 2022)Accurate prediction of the subcellular locations (SLs) of proteins is a critical topic in protein science. In this study, we present SLPred, an ensemble-based multi-view and multi-label protein subcellular localization ... -
Transfer learning for drug–target interaction prediction
Dalkıran, Alperen; Atakan, Ahmet; Rifaioğlu, Ahmet Süreyya; Martin, Maria Jesús; Atalay, Rengül Çetin; Acar, Aybar Can; Doǧan, Tunca; Atalay, Volkan (Oxford University Press, 2023)MotivationUtilizing AI-driven approaches for drug-target interaction (DTI) prediction require large volumes of training data which are not available for the majority of target proteins. In this study, we investigate the ...