Computer simulation of protein folding

@article{Levitt1975ComputerSO,
  title={Computer simulation of protein folding},
  author={Michael Levitt and Arieh Warshel},
  journal={Nature},
  year={1975},
  volume={253},
  pages={694-698}
}
A new and very simple representation of protein conformations has been used together with energy minimisation and thermalisation to simulate protein folding. Under certain conditions, the method succeeds in ‘renaturing’ bovine pancreatic trypsin inhibitor from an open-chain conformation into a folded conformation close to that of the native molecule. 
Folding and association of proteins.
  • R. Jaenicke
  • Biology
    Biophysics of structure and mechanism
  • 1982
Protein folding and unfolding.
  • F. Pohl
  • Biology, Chemistry
    Molecular biology, biochemistry, and biophysics
  • 1977
TLDR
The elucidation of the pathways of folding, the magnitude of the different thermodynamic forces involed, and the kinetics of such processes are still in a relatively early stage of investigation.
Solvation energy in protein folding and binding
TLDR
A method for calculating the stability in water of protein structures, starting from their atomic coordinates, as the product of the accessibility of the atom to solvent and its atomic solvation parameter is developed.
Folding Polymer Chains
Molecular dynamics simulations are used to study helix formation in a simple model polymer chain that is subject to excluded volume and torsional interactions. The changing conformations exhibited by
Protein-folding dynamics
In a discussion of the dynamics of protein folding two limiting models (random-search nucleation and chain propagation., diffusion–collision) are considered. It is suggested that the latter may have
Prediction of protein structure from amino acid sequence
TLDR
This work uses simple models to represent protein conformation and interatomic interactions, together with the knowledge gained from analyses of known protein structures to predict the three-dimensional structure of a protein from its amino acid sequence.
Calculation of protein tertiary structure.
A computer model to dynamically simulate protein folding: Studies with crambin
TLDR
Many characteristics expected of true proteins, such as the sequence‐dependent formation of secondary structure, the partitioning of hydrophobic residues, and specific disulfide, are suggested so that the model may accurately simulate the folding process.
Characteristic temperatures of folding of a small peptide.
TLDR
It is shown that the folding of a small peptide is a multistage process associated with two characteristic temperatures, the collapse temperature Ttheta and the folding temperature T, which gives supporting evidence for the energy landscape picture and funnel concept.
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References

SHOWING 1-10 OF 42 REFERENCES
Principles that govern the folding of protein chains.
TLDR
In his Nobel Lecture, Anfinsen provided a sketch of the rich history of research that provided the foundation for his work on protein folding and the "Thermodynamic Hypothesis," and outlined potential avenues of current and future scientific exploration.
Microscopic model for the study of fluctuations and the kinetics of conformational changes of polypeptides. I. Diglycine
TLDR
A microscopic model is developed which considers conformational changes in polypeptides and a first passage‐time treatment is developed and used to compute internal diffusion coefficients for the relaxation process.
Comparison of predicted and experimentally determined secondary structure of adenyl kinase
TLDR
The aim of this paper is to demonstrate directly the current standing of prediction schemes for the prediction of secondary structures in globular proteins from amino acid sequences, and to suggest new approaches to structure elucidation.
The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale.
TLDR
The results show the similarity between the effects of ethanol and dioxane on the stability of those side chains and peptide units, and have been used to establish a hydrophobicity scale for hydrophobic side chains.
Current Topics In Biochemistry.
TLDR
The book is based on a series of lectures held at the National Institutes of Health, Bethesda, Md during September 1971 to give up-to-date information about basic scientific research to young physicians who came to NIH for advanced training in biomedical research.
Biochemistry
  • F. Young
  • Education
    The Indian Medical Gazette
  • 1955
The Department of Biochemistry is internationally recognized for its research and education and offers a world-class interdisciplinary research environment in a beautiful mountain setting. As part of
Ciba Foundation Symposium
TLDR
The Ciba Foundation Symposium entitled "Cardiomyopathies" is timely because it has brought together a number of investigators whose deliberations are recorded in an orderly fashion in this volume.
...
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