The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
The Protein Folding Network
Abstract
The conformation space of a 20 residue antiparallel beta-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Snapshots saved along the trajectory are grouped according to secondary structure into nodes of the network and the transitions between them are links. The conformation space network describes the significant free energy minima and their dynamic connectivity without requiring arbitrarily chosen reaction coordinates. As previously found for the Internet and the World-Wide Web as well as for social and biological networks, the conformation space network is scale-free and contains highly connected hubs like the native state which is the most populated free energy basin. Furthermore, the native basin exhibits a hierarchical organization, which is not found for a random heteropolymer lacking a predominant free-energy minimum. The network topology is used to identify conformations in the folding transition state (TS) ensemble, and provides a basis for understanding the heterogeneity of the TS and denatured state ensemble as well as the existence of multiple pathways.
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Cites
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Cited by
Markov models of molecular kinetics: Generation and validation
Prinz, J.-H., Wu, H., Sarich, M., Keller, B., Senne, M., Held, M., Chodera, J. D., Schütte, C., & Noé, F. (2011) · The Journal of Chemical Physics · doi:10.1063/1.3565032 · Cited by 1,275
Identification of slow molecular order parameters for Markov model construction
Pérez-Hernández, G., Paul, F., Giorgino, T., De Fabritiis, G., & Noé, F. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4811489 · Cited by 990
“Kinetic models usually first partition the conformation space into discrete states [93, 61, 40, 33, 94, 14, 74, 56, 21, 80, 69].”
BackgroundStructure 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
Analyzing and modeling real-world phenomena with complex networks: a survey of applications
Costa, L. D. F., Oliveira, O. N., Travieso, G., Rodrigues, F. A., Villas Boas, P. R., Antiqueira, L., Viana, M. P., & Correa Rocha, L. E. (2011) · Advances in Physics · doi:10.1080/00018732.2011.572452 · Cited by 800
Detecting Fuzzy Community Structures in Complex Networks with a Potts Model
Reichardt, J., & Bornholdt, S. (2004) · Physical Review Letters · doi:10.1103/physrevlett.93.218701 · Cited by 593
Metadata
- Authors
- Rao, F., & Caflisch, A.
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2004-09
- Volume
- 342
- Issue
- 1
- Pages
- 299-306
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W1986155795
- Cited by
- 358
- References
- 38
- FWCI
- 6.12
- Type
- journal article
- Language
- en
- Open access
- closed
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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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