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Defining the protein interaction network of human malaria parasite Plasmodium falciparum

Abhinay Ramaprasad, Arnab Pain, Timothy Ravasi
2012 Genomics  
analysis of the PPI network.  ...  A proteinprotein interaction (PPI) network seeks to trace the dynamic interactions between proteins, thereby elucidating their local and global functional relationships.  ...  Fig. 2 . 2 The general methodology for inferring a P. falciparum protein-protein interaction network. Table 1 1 An overview of computational inference and analysis of malaria PPI network till date.  ... 
doi:10.1016/j.ygeno.2011.11.006 pmid:22178265 fatcat:774lkkr73fetnbs3bu26rqp6zi

Topological Characterization of Protein-Protein Interaction Networks in Human and Mouse

Bipin Singh
2011 Nature Precedings  
The elucidation of the cell's large-scale organization is a primary challenge for post-genomic biology, and understanding the structure and topological properties of protein-protein interaction networks  ...  We show that both human and mouse protein-protein interaction supports a scale-free, topology with hierarchical modularity, indicating that these features represent a robust and generic property of the  ...  The fast development of experimental techniques for protein interactions has enabled the construction and systematic analysis of interaction networks.  ... 
doi:10.1038/npre.2011.6126.1 fatcat:56h5bhfrpncxfooogobk5enpse

Statistical characteristics of amino acid covariance as possible descriptors of viral genomic complexity

C. K. Sruthi, Meher K. Prakash
2019 Scientific Reports  
Our host-virus interaction analysis point to the possibility that host proteins which can interact with multiple viral proteins may be responsible for shaping the inter-protein covariance relations.  ...  Simple because they have barely around 10 types of proteins, so viral protein-protein interaction networks are not insightful.  ...  The analysis represented in Fig. 6 shows that the viral proteins are clustered closely in dengue and influenza interactomes because many of the host proteins interact with more than one viral protein  ... 
doi:10.1038/s41598-019-54720-y pmid:31804522 pmcid:PMC6895170 fatcat:brfed44e4vg3jlrqbfg7c6xamu

Visualisation and graph-theoretic analysis of a large-scale protein structural interactome

Dan Bolser, Panos Dafas, Richard Harrington, Jong Park, Michael Schroeder
2003 BMC Bioinformatics  
Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network.  ...  More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution  ...  In this analysis, each edge in the network is equated with a state transition in a Markov process. A similar approach has been used for the analysis of clusters in a network [55] .  ... 
doi:10.1186/1471-2105-4-45 pmid:14531933 pmcid:PMC272926 fatcat:zwizfwsssbgx5oxy2zrqibypnu

Systems Proteomics for Translational Network Medicine

D. K. Arrell, A. Terzic
2012 Circulation: Cardiovascular Genetics  
Sources of Funding The authors are supported by National Institutes of Health, Marriott Foundation, Fondation Leducq, and Mayo Clinic. Disclosures None.  ...  Acknowledgments We thank our colleagues for helpful discussions.  ...  modification analysis strategies, eg, phosphopeptide enrichment, 21 plus continued growth and extensive curation of protein databases for comparison and identification of peptides and proteins from acquired  ... 
doi:10.1161/circgenetics.110.958991 pmid:22896016 pmcid:PMC3466103 fatcat:hudrukaw5je4bfanb4hlcyjege

Topological robustness analysis of protein interaction networks reveals key targets for overcoming chemotherapy resistance in glioma

Hátylas Azevedo, Carlos Alberto Moreira-Filho
2015 Scientific Reports  
Highly connected nodes are called hubs and they tend to be essential in protein interaction networks 5 , highlighting the importance of hierarchy for the functioning of molecular pathways.  ...  Here, we built protein interaction networks associated with chemoresistance to temozolomide, an alkylating agent used in glioma therapy, and analyzed their modular structure and robustness against intentional  ...  Acknowledgements This work was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo-FAPESP (grant 2011/50761-2), Conselho Nacional de Desenvolvimento Cientifico e Tecnológico-CNPq (grant 307626/2014-8) and  ... 
doi:10.1038/srep16830 pmid:26582089 pmcid:PMC4652178 fatcat:dk7pdx2i7bc4dmouxvwbh5oi5m

Data Sources and Computational Approaches for Generating Models of Gene Regulatory Networks [chapter]

Baltazar D. Aguda, Georghe Craciun, Rengul Cetin-Atalay
2005 Reviews in computational chemistry  
Cytoscape and PathwayAssist are similar software tools for automated analysis, integration and visualization of protein interaction maps.  ...  PATHWAYS DATABASES AND PLATFORMS Along with recent advances in genomics and proteomics, requirements for analysis, expansion and visualization of cell signaling, GRNs and protein-protein interaction maps  ... 
doi:10.1002/0471720895.ch6 fatcat:iaodscfur5e3pjy2z2oejtufyy

Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network

Christine Brun, François Chevenet, David Martin, Jérôme Wojcik, Alain Guénoche, Bernard Jacq
2003 Genome Biology  
We here describe PRODISTIN, a new computational method allowing the functional clustering of proteins on the basis of protein-protein interaction data.  ...  biological process(es), and to predict a cellular function for many otherwise uncharacterized proteins.  ...  Thieffry for carefully reading the manuscript and helpful discussions, and Pierre Mouren for technical assistance.  ... 
doi:10.1186/gb-2003-5-1-r6 pmid:14709178 pmcid:PMC395738 fatcat:psgnmbhgojdbvfdzeg7gfscrmi

The NRGTEN Python package: an extensible toolkit for coarse-grained normal mode analysis of proteins, nucleic acids, small molecules and their complexes [article]

Olivier Mailhot, Rafael Najmanovich
2020 arXiv   pre-print
The inclusion of the ENCoM model (Elastic Network Contact Model) developed in our group within NRGTEN is noteworthy, owing to its account for the specific chemical nature of atomic interactions.  ...  Furthermore, the toolkit is available as a public Python package and is easily extensible for the development or implementation of additional NMA models.  ...  Conclusions We have developed the Najmanovich Research Group Toolkit for Elastic Networks (NRGTEN), an expanded, extensible and user-friendly toolkit for coarse-grained elastic networks as a Python package  ... 
arXiv:2012.13062v1 fatcat:5suvoklsjjcc7mscmbzzaqq3mi

Random network behaviour of protein structures

K. V. Brinda, Saraswathi Vishveshwara, Smitha Vishveshwara
2010 Molecular Biosystems  
Thus, within the rigid framework of the protein backbone that restricts the structure space, the side-chain interactions exhibit an element of randomness, which account for the functional flexibility and  ...  Here, we focus on side-chain interactions, which non-covalently link amino acids in folded proteins to form a network structure.  ...  DMR 06-44022 CAR and the Mathematical Biology project funded by the Department of Science and Technology (DST), India for computational facilities.  ... 
doi:10.1039/b903019k pmid:20094659 fatcat:bvbuok4bjrh5zp6q6mxgseihdq

Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N

Polydefkis Diamantis, Oliver T. Unke, Markus Meuwly, Alexander MacKerell
2017 PLoS Computational Biology  
A quantitative assessment of ligand diffusion in these networks is thus essential for a better understanding of the function of these proteins.  ...  Transitions between pockets of the migration network and intra-pocket relaxation occur on similar time scales (10 ps and 20 ps), consistent with low free energy barriers (1-2 kcal/mol).  ...  Extensive research has shown that such networks of internal cavities (pockets, packing defects) exist particularly in globular proteins, and has been confirmed for heme containing proteins including myoglobin  ... 
doi:10.1371/journal.pcbi.1005450 pmid:28358830 pmcid:PMC5391117 fatcat:o72xduczrzcftm33utf43a3tni

Communication between levels of transcriptional control improves robustness and adaptivity

Alexander M Tsankov, Christopher R Brown, Michael C Yu, Moe Z Win, Pamela A Silver, Jason M Casolari
2006 Molecular Systems Biology  
Analysis of the regulatory network also reveals an elegant architecture for transcriptional control.  ...  Moreover, we provide evidence that communication between different regulatory groups improves the robustness and adaptivity of the cell.  ...  We thank Jessica Hurt, Natalie Farny, and Jake Wintermute for critical reading of the manuscript.  ... 
doi:10.1038/msb4100106 pmid:17130867 pmcid:PMC1682026 fatcat:rmznoquhhbfwvkngdq4yr65e6i

Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae

M. R. Said, T. J. Begley, A. V. Oppenheim, D. A. Lauffenburger, L. D. Samson
2004 Proceedings of the National Academy of Sciences of the United States of America  
study of how protein-protein interaction network characteristics may be associated with phenotypic functional effects.  ...  Here, we present a global network investigation of the genotype͞ phenotype data set we developed for the recovery of the yeast Saccharomyces cerevisiae from exposure to DNA-damaging agents, enabling explicit  ...  The clustering coefficient, C, can be determined for each protein to identify the degree of connectivity between a given protein's neighbors. (B) Clustering coefficient analysis.  ... 
doi:10.1073/pnas.0405996101 pmid:15608068 pmcid:PMC539745 fatcat:mut23chd65hfdljxrj6a5ng7iy

A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface

Gagan D. Gupta, Étienne Coyaud, João Gonçalves, Bahareh A. Mojarad, Yi Liu, Qianzhu Wu, Ladan Gheiratmand, David Comartin, Johnny M. Tkach, Sally W.T. Cheung, Mikhail Bashkurov, Monica Hasegan (+8 others)
2015 Cell  
Graphical Abstract Highlights d BioID conducted on 58 centriole, satellite, and ciliary transition zone proteins d Centriole-cilium interface map comprises >1,700 unique components, >7,000 interactions  ...  d Microscopy and functional screens confirm new centriolecilium regulatory modules d Dynamic modulation of interaction landscape observed during ciliogenesis program  ...  The clustering of NPHP1 and NPHP4 in Tz1 and TMEM67 and TMEM237 in Tz2, and the separation of Tz1 and Tz2 in our network is also consistent with the reported hierarchy of interactions within the transition  ... 
doi:10.1016/j.cell.2015.10.065 pmid:26638075 pmcid:PMC5089374 fatcat:av27mndmrbcbldbygtus3mc5ay

An automated approach to network features of protein structure ensembles

Moitrayee Bhattacharyya, Chanda R. Bhat, Saraswathi Vishveshwara
2013 Protein Science  
PSN-Ensemble serves as a robust, standalone program, which can easily compute the network features from a protein structure in an automated and userfriendly manner.  ...  Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active=inactive states of b2-adrenergic receptor and the ternary tRNA complexes of tyrosyl  ...  Acknowledgments S.V. and M.B. thanks CSIR for emeritus professorship and fellowship, respectively.  ... 
doi:10.1002/pro.2333 pmid:23934896 pmcid:PMC3795498 fatcat:qmwqltcsjrcstlirlp4fzurd3q
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