Open Access. Powered by Scholars. Published by Universities.®
- Institution
- Keyword
-
- Protein domain annotation, Gene prediction (2)
- Protein folding (2)
- Algorithms (1)
- Alpha helical proteins (1)
- Bayes theorem (1)
-
- Bioinformatics (1)
- Chemistry (1)
- Death domain superfamily (1)
- Disulfides (1)
- Eukarya (1)
- Functional genome annota- tion (1)
- GO classification (1)
- Greek-key topology (1)
- HMM models (1)
- Humans (1)
- Hydrophobic residues (1)
- Immunoglobulin (1)
- Informatics (1)
- Ligand-independent Activity; Microarray Screen; Heregulin; Anti-adhesion; Heterodimer; Phosphorylation; ErbB2 Signaling; Receptor Tyrosine Kinase; Membrane Mucin; Muc4; Epidermal Growth Factor Receptor (1)
- Post-doc work (1)
- Probability (1)
- Protein domains (1)
- Protein structure (1)
- Proteins (1)
- RT PCR (1)
- Reverse transcription polymerase chain reaction (1)
- Secondary (1)
- Software (1)
- Publication
- Publication Type
- File Type
Articles 1 - 7 of 7
Full-Text Articles in Biochemistry
Planning Combinatorial Disulfide Cross-Links For Protein Fold Determination, Fei Xiong, Alan M Friedman, Chris Bailey-Kellogg
Planning Combinatorial Disulfide Cross-Links For Protein Fold Determination, Fei Xiong, Alan M Friedman, Chris Bailey-Kellogg
Dartmouth Scholarship
Fold recognition techniques take advantage of the limited number of overall structural organizations, and have become increasingly effective at identifying the fold of a given target sequence. However, in the absence of sufficient sequence identity, it remains difficult for fold recognition methods to always select the correct model. While a native-like model is often among a pool of highly ranked models, it is not necessarily the highest-ranked one, and the model rankings depend sensitively on the scoring function used. Structure elucidation methods can then be employed to decide among the models based on relatively rapid biochemical/biophysical experiments.
Muc4 Modulation Of Ligand-Independent Erbb2 Signaling, Goldi Attias Kozloski
Muc4 Modulation Of Ligand-Independent Erbb2 Signaling, Goldi Attias Kozloski
Goldi A Kozloski
The membrane mucin Muc4 is a heterodimer, bi-functional glycoprotein complex that is normally expressed in epithelial tissue. Functional studies on the extracellular mucin subunit of Muc4 have shown that it acts to promote anti-adhesion properties by sterically interfering with cell-cell and cell-matrix interactions and that the extent of this effect is directly associated with the number of tandem repeats on this subunit. Functional studies on the transmembrane subunit of Muc4 have shown that this subunit participates in intracellular signaling through interaction with the receptor tyrosine kinase ErbB2. This role of Muc4 was shown to be mediated by stabilizing the heregulin …
Micrornas Are Independent Predictors Of Outcome In Diffuse Large B-Cell Lymphoma Patients Treated With R-Chop, Goldi Kozloski
Micrornas Are Independent Predictors Of Outcome In Diffuse Large B-Cell Lymphoma Patients Treated With R-Chop, Goldi Kozloski
Goldi A Kozloski
Practical Approach To Bioinformatics, Nigel Yarlett, Melissa Grigione
Practical Approach To Bioinformatics, Nigel Yarlett, Melissa Grigione
Cornerstone 3 Reports : Interdisciplinary Informatics
No abstract provided.
Bioinformatics, Thermodynamics And Kinetics Analysis Of An All Alpha Helical Protein With A Gree-Key Topology, Hai Li
Chemistry & Biochemistry Theses & Dissertations
Computational and experimental studies focusing on the role of conserved residues for folding and stability is an active and promising area of research. To further expand our understanding we present the results of a bioinformatics analysis of the death domain superfamily. The death domain superfamily fold consists of six α-helices arranged in a Greek-key topology, which is shared by the all β-sheet immunoglobulin and mixed α/β-plait superfamilies. Our sequence and structural studies have identified a group of conserved hydrophobic residues and corresponding long-range interactions, which we propose are important in the formation and stabilization of the hydrophobic core and native …
Evolution And Quantitative Comparison Of Genome-Wide Protein Domain Distributions, Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska
Evolution And Quantitative Comparison Of Genome-Wide Protein Domain Distributions, Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska
Arli A Parikesit
The metabolic and regulatory capabilities of an organism are implicit in its protein content. This is often hard to estimate, however, due to ascertainment biases inherent in the available genome annotations. Its complement of recognizable functional protein domains and their combinations convey essentially the same information and at the same time are much more readily accessible, although protein domain models trained for one phylogenetic group frequently fail on distantly related sequences. Pooling related domain models based on their GO-annotation in combination with de novo gene prediction methods provides estimates that seem to be less affected by phylogenetic biases. We show …
Evolution Of Domain Co-Occurrences: Some Striking Results, Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska
Evolution Of Domain Co-Occurrences: Some Striking Results, Arli A. Parikesit, Peter F. Stadler, Sonja J. Prohaska
Arli A Parikesit
No abstract provided.