The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Network analysis of protein dynamics
Open accessAbstract
The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here, we review the results of the topological analysis of protein structures as molecular networks describing their small‐world character, and the role of hubs and central network elements in governing enzyme activity, allosteric regulation, protein motor function, signal transduction and protein stability. We summarize available data how central network elements are enriched in active centers and ligand binding sites directing the dynamics of the entire protein. We assess the feasibility of conformational and energy networks to simplify the vast complexity of rugged energy landscapes and to predict protein folding and dynamics. Finally, we suggest that modular analysis, novel centrality measures, hierarchical representation of networks and the analysis of network dynamics will soon lead to an expansion of this field.
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Cites
Network biology: understanding the cell's functional organization
Barabási, A.-L., & Oltvai, Z. N. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1272 · Cited by 7,903
Uncovering the overlapping community structure of complex networks in nature and society
Palla, G., Derényi, I., Farkas, I., & Vicsek, T. (2005) · Nature · doi:10.1038/nature03607 · Cited by 5,373
Hierarchical Organization of Modularity in Metabolic Networks
Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N., & Barabási, A.-L. (2002) · Science · doi:10.1126/science.1073374 · Cited by 4,224
Protein states and proteinquakes.
Ansari, A., Berendzen, J., Bowne, S. F., Frauenfelder, H., Iben, I. E., Sauke, T. B., Shyamsunder, E., & Young, R. D. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.15.5000 · Cited by 828
Cited by
Structure and dynamics of molecular networks: A novel paradigm of drug discovery
Csermely, P., Korcsmáros, T., Kiss, H. J. M., London, G., & Nussinov, R. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.01.016 · Cited by 892
Self-citationCsermely, P., Palotai, R., & Nussinov, R. (2010) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2010.04.009 · Cited by 821
Self-citationAllosteric regulation and catalysis emerge via a common route
Goodey, N. M., & Benkovic, S. J. (2008) · Nature Chemical Biology · doi:10.1038/nchembio.98 · Cited by 667
Molecular dynamics simulations and novel drug discovery
Liu, X., Shi, D., Zhou, S., Liu, H., Liu, H., & Yao, X. (2018) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2018.1403419 · Cited by 518
Topological analysis and interactive visualization of biological networks and protein structures
Doncheva, N. T., Assenov, Y., Domingues, F. S., & Albrecht, M. (2012) · Nature Protocols · doi:10.1038/nprot.2012.004 · Cited by 503
Metadata
- Authors
- Böde, C., Kovács, I. A., Szalay, M. S., Palotai, R., Korcsmáros, T., & Csermely, P.
- Venue
- FEBS Letters
- Publisher
- Wiley
- Published
- 2007-05-21
- Volume
- 581
- Issue
- 15
- Pages
- 2776-2782
- ISSN
- 0014-5793 (ISSN-L)
- 1873-3468
- OpenAlex
- W2007268492
- Cited by
- 223
- References
- 4
- FWCI
- 4.31
- Type
- journal article
- Language
- en
- Open access
- green
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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