منابع مشابه
Exploring protein energy landscapes with hierarchical clustering.
In this work we present a new method for investigating local energy minima on a protein energy landscape. The CABS (CAlpha, CBeta and the center of mass of the Side chain) method was employed for generating protein models, but any other method could be used instead. Cα traces from an ensemble of models are hierarchical clustered with the HCPM (Hierarchical Clustering of Protein Models) method. ...
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Human diseases, such as Alzheimer's and Creutzfeldt-Jakob's are associated with misfolding and aggregation of specific proteins into amyloid fibrils sharing a generic cross-beta structure. The self-assembly process is complex, but once a nucleus is formed, rapid fibril formation occurs. Insight into the structures of the oligomers during the lag phase, varying between hours and days, is very di...
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Recent advances in computational protein design have allowed exciting new insights into the sequence dependence of protein folding free energy landscapes. Whereas most previous studies have examined the sequence dependence of protein stability and folding kinetics by characterizing naturally occurring proteins and variants of these proteins that contain a small number of mutations, it is now po...
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Local minima and the saddle points separating them in the energy landscape are known to dominate the dynamics of biopolymer folding. Here we introduce a notion of a “folding funnel” that is concisely defined in terms of energy minima and saddle points, while at the same time conforming to a notion of a “folding funnel” as it is discussed in the protein folding literature. PACS. 87.10.+e General...
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The multidimensional potential-energy “landscape” formalism offers useful insights into the properties of supercooled liquids and glasses. However, its mathematical fundamentals present formidable subtlety and complexity. In the interests of developing a useful approximation for the statistical mechanics of landscapes, we have developed a simple family of models describing the energy-depth dist...
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ژورنال
عنوان ژورنال: Annual Review of Physical Chemistry
سال: 2018
ISSN: 0066-426X,1545-1593
DOI: 10.1146/annurev-physchem-050317-021219