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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Initial Characterization Of A Conserved Active Site Residue For The Cdc34 Ubiquitin Conjugating Enzyme, Arvin Akoopie
Initial Characterization Of A Conserved Active Site Residue For The Cdc34 Ubiquitin Conjugating Enzyme, Arvin Akoopie
Honors College Theses
Ubiquitin-conjugating enzymes (E2s) covalently modify protein substrates with ubiquitins. The active site cysteine residues on E2s are essential for catalyzing the transfer of ubiquitin from the E2 active site onto the protein substrate, however there is a limited amount of information available concerning additional active site residues for E2s that may also participate in catalysis. Cdc34 is an essential E2 that has merited the lion’s share of attention for biochemical analysis of the E2 family. Previous phylogenetic analysis of Cdc34 amino acid sequences has identified an invariably conserved histidine residue close to the active site cysteine in the primary structure, …
Template-Based C8-Scorpion: A Protein 8 State Secondary Structure Prediction Method Using Structural Information And Context-Based Features, Ashraf Yaseen, Yaohang Li
Template-Based C8-Scorpion: A Protein 8 State Secondary Structure Prediction Method Using Structural Information And Context-Based Features, Ashraf Yaseen, Yaohang Li
Computer Science Faculty Publications
Background: Secondary structures prediction of proteins is important to many protein structure modeling applications. Correct prediction of secondary structures can significantly reduce the degrees of freedom in protein tertiary structure modeling and therefore reduces the difficulty of obtaining high resolution 3D models.
Methods: In this work, we investigate a template-based approach to enhance 8-state secondary structure prediction accuracy. We construct structural templates from known protein structures with certain sequence similarity. The structural templates are then incorporated as features with sequence and evolutionary information to train two-stage neural networks. In case of structural templates absence, heuristic structural information is incorporated instead. …