Tez No	İndirme	Tez Künye	Durumu
401700		Protein docking refinement using evolutionary information and artificial intelligence / Yazar:AYŞE BAHAR Danışman: YRD. DOÇ. DR. NURIT HASPEL Yer Bilgisi: THE UNIVERSITY OF MASSACHUSETTS BOSTON / YURTDIŞI ENSTİTÜ / BİLGİSAYAR BİLİMLERİ VE MÜHENDİSLİĞİ ANABİLİM DALI Konu:Bilgisayar Mühendisliği Bilimleri-Bilgisayar ve Kontrol = Computer Engineering and Computer Science and Control Anahtar Kelime:	Onaylandı Doktora İngilizce 2014 163 s.
The immense amount of data generated since the onset of the post-genomic era has affected all fields of computational biology, including the study of protein-protein interactions. Databases of experimentally identified protein complexes provide a gold standard test for developing accurate models of undiscovered protein complexes. However, protein-protein docking methods still suffer from the prevalence of false positives among their results. Using evolutionary conservation information and artificial intelligence techniques, this thesis proposes four related methods for obtaining more native-like conformations in protein-protein docking as well as detecting residues that are critical for protein structure and function. First, two stochastic methods for refining docked dimeric and multimeric complexes are introduced. Then, a novel machine learning based tool is presented to predict the structural similarity of a docked protein complex to its native form. Using this tool for ranking decoys, a third method is proposed to refine docked protein complexes. Finally, combining evolutionary information with protein rigidity analysis, another machine-learning based method is presented for predicting critical protein residues, which can play an important role in protein-protein binding.