scholarly journals A novel approach for the identification of protein-protein interaction with integral membrane proteins

2001 ◽  
Vol 29 (4) ◽  
pp. 18e-18 ◽  
Author(s):  
M. Hubsman
Keyword(s):  
Membrane Proteins ◽  
Protein Interaction ◽  
Integral Membrane Proteins ◽  
Protein Protein Interaction ◽  
Novel Approach

scholarly journals Novel approach to protein-protein interaction assessment

2020 ◽  
Vol 548 ◽  
pp. 072046
Author(s):  
F N Gilmiyarova ◽  
N A Kolotyeva ◽  
V I Kuzmicheva ◽  
V V Remizov ◽  
O A Gusyakova
Keyword(s):  
Protein Interaction ◽  
Protein Protein Interaction ◽  
Novel Approach

scholarly journals From phages to mammalian viruses: viral receptors play a central role in protein-protein interaction network

2019 ◽  
Author(s):  
Fen Yu ◽  
Zheng Zhang ◽  
Yuanqiang Zou ◽  
Ye Qiu ◽  
Aiping Wu ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Protein Interaction ◽  
Outer Membrane Proteins ◽  
Host Cells ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
Virus Receptors ◽  
Protein Receptors ◽  
Mammalian Virus

AbstractMotivationReceptors on host cells play a critical role in viral infection. How phages select receptors is still unknown.ResultsHere, we manually curated a high-quality database named phageReceptor, including 355 pairs of phage-host receptor interactions, 280 unique viral species or sub-species and 64 bacterial species. Sugars and proteins were most widely used by phages as receptors. The receptor usage of phages in Gram-positive bacteria was different from that in Gram-negative bacteria. Most protein receptors were located on the outer membrane. The protein receptors were highly diverse in their structures, and had little homology with mammalian virus receptors. Further functional characterization of phage protein receptors in Escherichia coli showed that they had larger node degrees and betweennesses in the protein-protein interaction (PPI) network, and higher expression levels, than other outer membrane proteins, plasma membrane proteins, or other intracellular proteins. These findings were consistent with what observed for mammalian virus receptors, suggesting that viral protein receptors play a central role in the host’s PPI network. The study deepens our understanding of virus-host interactions.AvailabilityThe database of phageReceptor is publicly accessible at http://www.computationalbiology.cn/viralRecepetor/index.html.

Membrane-SPINE: An improved method to identify protein-protein interaction partners of membrane proteins in vivo

PROTEOMICS ◽  
2011 ◽  
Vol 11 (10) ◽  
pp. 2124-2128 ◽  
Author(s):  
Volker S. Müller ◽  
Peter R. Jungblut ◽  
Thomas F. Meyer ◽  
Sabine Hunke
Keyword(s):  
Membrane Proteins ◽  
Protein Interaction ◽  
Improved Method ◽  
Protein Protein Interaction ◽  
Interaction Partners

scholarly journals A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Meijing Li ◽  
Tsendsuren Munkhdalai ◽  
Xiuming Yu ◽  
Keun Ho Ryu
Keyword(s):  
Language Processing ◽  
Protein Interaction ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Support Vector ◽  
Protein Protein Interaction ◽  
Named Entity ◽  
Novel Approach ◽  
Interaction Extraction ◽  
Parsing Tree

Many researchers focus on developing protein-named entity recognition (Protein-NER) or PPI extraction systems. However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve. In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM) and parsing tree. PPIMiner consists of three main models: natural language processing (NLP) model, Protein-NER model, and PPI discovery model. The Protein-NER model, which is named ProNER, identifies the protein names based on two methods: dictionary-based method and machine learning-based method. ProNER is capable of identifying more proteins than dictionary-based Protein-NER model in other existing systems. The final discovered PPIs extracted via PPI discovery model are represented in detail because we showed the protein interaction types and the occurrence frequency through two different methods. In the experiments, the result shows that the performances achieved by our ProNER and PPI discovery model are better than other existing tools. PPIMiner applied this protein-named entity recognition approach and parsing tree based PPI extraction method to improve the performance of PPI extraction. We also provide an easy-to-use interface to access PPIs database and an online system for PPIs extraction and Protein-NER.

Image Analysis of Intramembrane Particles in Freeze-Fractured Biomembranes Using Computer Simulation Techniques

1975 ◽  
Vol 33 ◽  
pp. 214-215
Author(s):  
D.J. Benefiel ◽  
R.S. Weinstein
Keyword(s):  
Membrane Proteins ◽  
Freeze Fracture ◽  
Integral Membrane Proteins ◽  
Systematic Evaluation ◽  
Intramembrane Particles ◽  
Modeling Methods ◽  
Simulation Techniques ◽  
Freeze Fracture Electron Microscopy ◽  
Fracture Electron ◽  
Computer Simulation Techniques

Intramembrane particles (IMP or MAP) are components of most biomembranes. They are visualized by freeze-fracture electron microscopy, and they probably represent replicas of integral membrane proteins. The presence of MAP in biomembranes has been extensively investigated but their detailed ultrastructure has been largely ignored. In this study, we have attempted to lay groundwork for a systematic evaluation of MAP ultrastructure. Using mathematical modeling methods, we have simulated the electron optical appearances of idealized globular proteins as they might be expected to appear in replicas under defined conditions. By comparing these images with the apearances of MAPs in replicas, we have attempted to evaluate dimensional and shape distortions that may be introduced by the freeze-fracture technique and further to deduce the actual shapes of integral membrane proteins from their freezefracture images.

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