ArticleProceedings of the National Academy of Sciences of the United States of America2012
Folding helical proteins in explicit solvent using dihedral-biased tempering.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Computational methods for exploring protein conformations.Biochemical Society transactions · 2020Review
- Refining protein structures using enhanced sampling techniques with restraints derived from an ensemble-based model.Protein science : a publication of the Protein Society · 2018Article
- Improving low-accuracy protein structures using enhanced sampling techniques.The Journal of chemical physics · 2018Article
- Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Conversion between parallel and antiparallel β-sheets in wild-type and Iowa mutant AβThe Journal of chemical physics · 2018Article
- Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins.The journal of physical chemistry. B · 2017Article
- Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.The journal of physical chemistry. B · 2016Article
- Dynamics of the BH3-Only Protein Binding Interface of Bcl-xL.Biophysical journal · 2015Article
- Targeting electrostatic interactions in accelerated molecular dynamics with application to protein partial unfolding.Journal of chemical theory and computation · 2015Article
- Parallel continuous simulated tempering and its applications in large-scale molecular simulations.The Journal of chemical physics · 2014Article
- Article
- The unsolved "solved-problem" of protein folding.Journal of biomolecular structure & dynamics · 2013Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
Abstract
Using a single-trajectory-based tempering method with a high-temperature dihedral bias, we repeatedly folded four helical proteins [α(3)D (PDB ID: 2A3D, 73 residues), α(3)W (1LQ7, 67 residues), Fap1-NR(α) (2KUB, 81 residues) and S-836 (2JUA, 102 residues)] and some of the mutants in explicit solvent within several microseconds. The lowest root-mean-square deviations of backbone atoms from the experimentally determined structures were 1.9, 1.4, 1.0, and 2.1 Å, respectively. Cluster analyses of folding trajectories showed the native conformation usually occupied the most populated cluster. The simulation protocol can be applied to large-scale simulations of other helical proteins on commonly accessible computing platforms.
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