Michael J. Sweredoski

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SCRATCH is a server for predicting protein tertiary structure and structural features. The SCRATCH software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. The user(More)
Intrinsically disordered regions in proteins are relatively frequent and important for our understanding of molecular recognition and assembly, and protein structure and function. From an algorithmic standpoint, flagging large disordered regions is also imortant for ab inito protein structure prediction methods. Here we first extract a curated,(More)
Parkin, an E3 ubiquitin ligase implicated in Parkinson's disease, promotes degradation of dysfunctional mitochondria by autophagy. Using proteomic and cellular approaches, we show that upon translocation to mitochondria, Parkin activates the ubiquitin-proteasome system (UPS) for widespread degradation of outer membrane proteins. This is evidenced by an(More)
MOTIVATION Accurate prediction of B-cell epitopes is an important goal of computational immunology. Up to 90% of B-cell epitopes are discontinuous in nature, yet most predictors focus on linear epitopes. Even when the tertiary structure of the antigen is available, the accurate prediction of B-cell epitopes remains challenging. RESULTS Our predictor,(More)
Protein domains are the structural and functional units of proteins. The ability to parse protein chains into different domains is important for protein classification and for understanding protein structure, function, and evolution. Here we use machine learning algorithms, in the form of recursive neural networks, to develop a protein domain predictor(More)
Motivation: Transmembrane-barrel (TMB) proteins are embedded in the outer membranes of mitochondria, Gram-negative bacteria, and chloroplasts. These proteins perform critical functions, including active ion-transport and passive nutrient intake. Therefore there is a need for accurate prediction of secondary and tertiary structure of TMB proteins.(More)
Many long non-coding RNAs (lncRNAs) affect gene expression, but the mechanisms by which they act are still largely unknown. One of the best-studied lncRNAs is Xist, which is required for transcriptional silencing of one X chromosome during development in female mammals. Despite extensive efforts to define the mechanism of Xist-mediated transcriptional(More)
synGAP is a neuron-specific Ras and Rap GTPase-activating protein (GAP) found in high concentrations in the postsynaptic density (PSD) fraction from the mammalian forebrain. We have previously shown that, in situ in the PSD fraction or in recombinant form in Sf9 cell membranes, synGAP is phosphorylated by Ca(2+)/calmodulin-dependent protein kinase II(More)
The human genome encodes 69 different F-box proteins (FBPs), each of which can potentially assemble with Skp1-Cul1-RING to serve as the substrate specificity subunit of an SCF ubiquitin ligase complex. SCF activity is switched on by conjugation of the ubiquitin-like protein Nedd8 to Cul1. Cycles of Nedd8 conjugation and deconjugation acting in conjunction(More)
Accurate prediction of B-cell epitopes has remained a challenging task in computational immunology despite several decades of research. Only 10% of the known B-cell epitopes are estimated to be continuous, yet they are often the targets of predictors because a solved tertiary structure is not required and they are integral to the development of peptide(More)