Yazar "Doğan, Tunca" için 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 ... -
DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks
Rifaioğlu, Ahmet Süreyya; Doğan, Tunca; Martin, Maria Jesus; Çetin-Atalay, Rengül; Atalay, Volkan (Nature Publishing Group, 2019)Automated protein function prediction is critical for the annotation of uncharacterized protein sequences, where accurate prediction methods are still required. Recently, deep learning based methods have outperformed ... -
DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations
Rifaioğlu, Ahmet Süreyya; Nalbat, Esra; Atalay, Volkan; Martin, Maria Jesus; Çetin-Atalay, Rengül; Doğan, Tunca (Royal Soc Chemistry, 2020)The identification of physical interactions between drug candidate compounds and target biomolecules is an important process in drug discovery. Since conventional screening procedures are expensive and time consuming, ... -
ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature
Dalkıran, Alperen; Rifaioğlu, Ahmet Süreyya; Martin, Maria Jesus; Çetin-Atalay, Rengül; Atalay, Volkan; Doğan, Tunca (BMC, 2018)Background: The automated prediction of the enzymatic functions of uncharacterized proteins is a crucial topic in bioinformatics. Although several methods and tools have been proposed to classify enzymes, most of these ... -
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, ... -
Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants
Rifaioğlu, Ahmet Süreyya; Doğan, Tunca; Saraç, Ömer Sinan; Erşahin, Tülin; Saidi, Rabie; Atalay, Mehmet Volkan; Martin, Maria Jesus; Atalay, Rengül Çetin (Wiley, 2018)Recent advances in computing power and machine learning empower functional annotation of protein sequences and their transcript variations. Here, we present an automated prediction system UniGOPred, for GO annotations and ... -
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 ... -
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 ... -
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases
Rifaioğlu, Ahmet Süreyya; Ataş, Heval; Martin, Maria Jesus; Çetin-Atalay, Rengül; Atalay, Volkan; Doğan, Tunca (Oxford Univ Press, 2019)The identification of interactions between drugs/compounds and their targets is crucial for the development of new drugs. In vitro screening experiments (i.e. bioassays) are frequently used for this purpose; however, ...
