Unsupervised identification of redundant domain entries in InterPro database using clustering techniques. - Ahmet Süreyya Rifaioglu; Tunca Dogan; Tolga Can (BCB, 2015)

ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature. - Alperen Dalkiran; Ahmet Süreyya Rifaioglu; Maria Jesus Martin; Rengül Çetin-Atalay; Volkan Atalay; Tunca Dogan (BMC Bioinform., 2018)

Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. - Ahmet Süreyya Rifaioglu; Heval Atas; Maria Jesus Martin; Rengül Çetin-Atalay; Volkan Atalay; Tunca Dogan (Briefings Bioinform., 2019)

iBioProVis: interactive visualization and analysis of compound bioactivity space. - Ataberk Donmez; Ahmet Süreyya Rifaioglu; Aybar C. Acar; Tunca Dogan; Rengül Çetin-Atalay; Volkan Atalay (Bioinform., 2020)

iBioProVis: interactive visualization and analysis of compound bioactivity space. - Ataberk Donmez; Ahmet Süreyya Rifaioglu; Aybar C. Acar; Tunca Dogan; Rengül Çetin-Atalay; Volkan Atalay; Wren Jonathan (Bioinform., 2020)

Deep learning for prediction of drug-target interaction space and protein functions (İlaç-hedef protein etkileşim uzayı ve protein fonksiyonlarının tahmini için derin öğrenme) - Ahmet Süreyya Rifaioglu (2020)

MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery. - Ahmet Süreyya Rifaioglu; Rengül Çetin-Atalay; Deniz Cansen Kahraman; Tunca Dogan; Maria Jesus Martin; Volkan Atalay (Bioinform., 2021)

SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins. - Gökhan Özsari; Ahmet Süreyya Rifaioglu; Ahmet Atakan; Tunca Dogan; Maria Jesus Martin; Rengül Çetin-Atalay; Volkan Atalay (Bioinform., 2022)

Transfer learning for drug-target interaction prediction. - Alperen Dalkiran; Ahmet Atakan; Ahmet Süreyya Rifaioglu; Maria Jesus Martin; Rengül Çetin-Atalay; Aybar C. Acar; Tunca Dogan; Volkan Atalay (Bioinform., 2023)

Target Specific De Novo Design of Drug Candidate Molecules with Graph Transformer-based Generative Adversarial Networks. - Atabey Ünlü; Elif Çevrim; Ahmet Sarigün; Hayriye Çelikbilek; Heval Atas Güvenilir; Altay Koyas; Deniz Cansen Kahraman; Abdurrahman Olgaç; Ahmet Süreyya Rifaioglu; Tunca Dogan (CoRR, 2023)

ProFAB - open protein functional annotation benchmark. - A Samet Özdilek; Ahmet Atakan; Gökhan Özsari; Aybar C. Acar; M. Volkan Atalay; Tunca Dogan; Ahmet Süreyya Rifaioglu (Briefings Bioinform., 2023)