Toward absolute density of states calculations for proteins

Article Abstract:

The total number of energy minima of 50-mer polyalanine whose size corresponds to naturally occurring proteins was estimated based on the cumulative distribution function (CDF) of conformational differences. It was shown that CDF can quantify conformational distribution and energy landscape by extension and can potentially restate the density of states of continuously variable protein models in terms of defined structural fluctuation.

Methods, Conformational analysis, Protein folding, Alanine, Structure, Chemical properties

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Potential energy and free energy landscapes

Article Abstract:

A study aims upon stationary points of the potential energy surface and the way they could be used to gain insight into structure, dynamics, and thermodynamics at both a qualitative and quantitative level. This coarse-grained approach provides the basis for calculations of global minima, global thermodynamics, and global kinetics through basin-hopping, basin sampling, and discrete path sampling.

Thermodynamics

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Design of a protein potential energy landscape by parameter optimization

Article Abstract:

An automated protocol is proposed for designing the energy landscape of a protein energy function by optimizing its parameters. The protocol is successfully applied to the parameter optimization of the UNRES potential energy using the training set of betanova, 1fsd, the 36-residue subdomain of chicken villin headpiece and the 10-55 residue fragment of staphylococcal protein A.

Proteins, Mathematical optimization, Optimization theory, Atomic properties

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