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Comprehensive Folding Variations for Protein Folding [PDF]
Proteins: Structure, Function, and Bioinformatics, 2022 The revelation of protein folding is a challenging subject in both discovery and description. Except acquirement of accurate 3D structure for protein stable state, another big hurdle is how to discover structural flexibility for protein innate character.
Jiaan Yang +10 more
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Protein folds and protein folding [PDF]
Protein Engineering Design and Selection, 2010 The classification of protein folds is necessarily based on the structural elements that distinguish domains. Classification of protein domains consists of two problems: the partition of structures into domains and the classification of domains into sets of similar structures (or folds).
R Dustin, Schaeffer, Valerie, Daggett
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Folding of Proteins with Diverse Folds [PDF]
Biophysical Journal, 2006 Using parallel tempering simulations with high statistics, we investigate the folding and thermodynamic properties of three small proteins with distinct native folds: the all-helical 1RIJ, the all-sheet beta3s, and BBA5, which has a mixed helix-sheet fold.
Mohanty, S., Hansmann, U. H. E.
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Progress in Nuclear Magnetic Resonance Spectroscopy, 2017 Protein folding is a highly complex process proceeding through a number of disordered and partially folded nonnative states with various degrees of structural organization. These transiently and sparsely populated species on the protein folding energy landscape play crucial roles in driving folding toward the native conformation, yet some of these ...
Zhuravleva, A, Korzhnev, DM
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On the kinematics of protein folding [PDF]
Journal of Computational Chemistry, 2003 AbstractWe offer simple solutions to three kinematic problems that occur in the folding of proteins. We show how to construct suitably local elementary Monte Carlo moves, how to close a loop, and how to fold a loop without breaking the bond that closes it. © 2003 Wiley Periodicals, Inc.
Sean Cahill +2 more
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Journal of Cellular and Molecular Medicine, 2003 AbstractThe problem of protein folding is that how proteins acquire their native unique three‐dimensional structure in the physiological milieu. To solve the problem, the following key questions should be answered: do proteins fold co‐ or post‐translationally, i.e.
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The Protein Folding Network [PDF]
Journal of Molecular Biology, 2004 The conformation space of a 20-residue antiparallel $β$-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 ...
Rao F, Caflisch A
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Folding nuclei in proteins [PDF]
FEBS Letters, 2001 When a protein folds or unfolds, it passes through many half‐folded microstates. Only a few of them can accumulate and be seen experimentally, and this happens only when the folding (or unfolding) occurs far from the point of thermodynamic equilibrium between the native and denatured states.
Galzitskaya, Oxana V +2 more
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The Protein Folding Problem [PDF]
Annual Review of Biophysics, 2008 The “protein folding problem” consists of three closely related puzzles: (a) What is the folding code? (b) What is the folding mechanism? (c) Can we predict the native structure of a protein from its amino acid sequence? Once regarded as a grand challenge, protein folding has seen great progress in recent years.
Dill, K. +3 more
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Chaos of protein folding [PDF]
The 2011 International Joint Conference on Neural Networks, 2011 As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that this folding process is predictable.
Jacques M. Bahi +2 more
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