Abstract
In this paper, the main achievements and problems of the application of all-atom molecular simulations, with particular attention for Molecular Dynamics (MD), will be critically reviewed. Starting from unfolding simulations, through biased simulations, which require a knowledge of the native state conformation, to folding studies based on the simple knowledge of the protein (or peptide) sequence, the strengths and weaknesses of theoretical approaches to the study of folding and their matching with experimental observations will be discussed. Finally, we will give a critical outlook on the possible developments of this field in the near future.
Keywords: nmr spectroscopy, biomolecules, simulation techniques, molecular dynamics (md), protein folding, atomic models, probe, thermodynamic, encephalopathies, noe constraints
Mini-Reviews in Medicinal Chemistry
Title: Folding and Mis-Folding of Peptides and Proteins: Insights from Molecular Simulations
Volume: 5 Issue: 4
Author(s): Giacomo M.S. De Mori, Massimiliano Meli, Luca Monticelli and Giorgio Colombo
Affiliation:
Keywords: nmr spectroscopy, biomolecules, simulation techniques, molecular dynamics (md), protein folding, atomic models, probe, thermodynamic, encephalopathies, noe constraints
Abstract: In this paper, the main achievements and problems of the application of all-atom molecular simulations, with particular attention for Molecular Dynamics (MD), will be critically reviewed. Starting from unfolding simulations, through biased simulations, which require a knowledge of the native state conformation, to folding studies based on the simple knowledge of the protein (or peptide) sequence, the strengths and weaknesses of theoretical approaches to the study of folding and their matching with experimental observations will be discussed. Finally, we will give a critical outlook on the possible developments of this field in the near future.
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Cite this article as:
De Mori M.S. Giacomo, Meli Massimiliano, Monticelli Luca and Colombo Giorgio, Folding and Mis-Folding of Peptides and Proteins: Insights from Molecular Simulations, Mini-Reviews in Medicinal Chemistry 2005; 5 (4) . https://dx.doi.org/10.2174/1389557053544038
DOI https://dx.doi.org/10.2174/1389557053544038 |
Print ISSN 1389-5575 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5607 |
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