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Combining experiment and simulation in protein folding: closing the gap for small model systems.
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Methods for molecular dynamics simulations of protein folding/unfolding in solution.
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Ten-microsecond molecular dynamics simulation of a fast-folding WW domain.
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Conformational dynamics and ensembles in protein folding.
Annu Rev Biophys Biomol Struct. 2007;36:395-412. doi: 10.1146/annurev.biophys.36.040306.132608.
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Folding of small proteins using constrained molecular dynamics.
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Coarse-grained models of protein folding: toy models or predictive tools?
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Molecular dynamics simulations of the protein unfolding/folding reaction.
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Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein.
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Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters.
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Intrinsic determinants of prion protein neurotoxicity in : from sequence to (dys)function.
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Coupled binding and folding of disordered SPIN N-terminal region in myeloperoxidase inhibition.
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Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments.
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Integrating Experiment and Theory to Understand TCR-pMHC Dynamics.
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CATS: A Tool for Clustering the Ensemble of Intrinsically Disordered Peptides on a Flat Energy Landscape.
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Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations.
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Complex Folding Landscape of Apomyoglobin at Acidic pH Revealed by Ultrafast Kinetic Analysis of Core Mutants.
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Modeling the mechanism of CLN025 beta-hairpin formation.
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Knotting and unknotting of a protein in single molecule experiments.
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3
A cross-strand Trp Trp pair stabilizes the hPin1 WW domain at the expense of function.
Protein Sci. 2007 Oct;16(10):2306-13. doi: 10.1110/ps.072904107. Epub 2007 Aug 31.
4
The role of the turn in beta-hairpin formation during WW domain folding.
Protein Sci. 2007 Oct;16(10):2233-9. doi: 10.1110/ps.073004907. Epub 2007 Aug 31.
6
Effects of crowding and confinement on the structures of the transition state ensemble in proteins.
J Phys Chem B. 2007 Jul 19;111(28):8250-7. doi: 10.1021/jp068201y. Epub 2007 Jun 22.
7
The helix-turn-helix motif as an ultrafast independently folding domain: the pathway of folding of Engrailed homeodomain.
Proc Natl Acad Sci U S A. 2007 May 29;104(22):9272-7. doi: 10.1073/pnas.0703434104. Epub 2007 May 18.
8
Two-stage folding of HP-35 from ab initio simulations.
J Mol Biol. 2007 Jun 29;370(1):196-206. doi: 10.1016/j.jmb.2007.04.040. Epub 2007 Apr 20.
9
Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation.
J Phys Chem B. 2007 May 17;111(19):5458-63. doi: 10.1021/jp0704867. Epub 2007 Apr 26.
10
Folding mechanisms of proteins with high sequence identity but different folds.
Biochemistry. 2007 Feb 13;46(6):1545-56. doi: 10.1021/bi061904l.

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