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Journal of Molecular Biology
Article . 2004 . Peer-reviewed
License: Elsevier TDM
Data sources: Crossref
https://dx.doi.org/10.48550/ar...
Article . 2004
License: arXiv Non-Exclusive Distribution
Data sources: Datacite
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The Protein Folding Network

Authors: Rao F; Caflisch A;

The Protein Folding Network

Abstract

The conformation space of a 20-residue antiparallel $��$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are 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 projections into 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 ensemble, and provides a basis for understanding the heterogeneity of the transition state and denaturated state ensemble as well as the existence of multiple pathway

Keywords

Models, Molecular, Protein Denaturation, Protein Folding, FOS: Physical sciences, Biomolecules (q-bio.BM), Disordered Systems and Neural Networks (cond-mat.dis-nn), Condensed Matter - Disordered Systems and Neural Networks, Models, Theoretical, Protein Structure, Secondary, Quantitative Biology - Biomolecules, FOS: Biological sciences, Thermodynamics, Peptides

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    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    328
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 1%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Top 1%
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 1%
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
328
Top 1%
Top 1%
Top 1%
Green
bronze