ArticleJournal of chemical information and modeling2014
Protein structure refinement of CASP target proteins using GNEIMO torsional dynamics method.
Article in Journal of chemical information and modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Methods for the Refinement of Protein Structure 3D Models.International journal of molecular sciences · 2019Review
- Experimental accuracy in protein structure refinement via molecular dynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling.Journal of chemical theory and computation · 2017Article
- Distinct structural mechanisms determine substrate affinity and kinase activity of protein kinase Cα.The Journal of biological chemistry · 2017Article
- Protein structure refinement via molecular-dynamics simulations: What works and what does not?Proteins · 2016Article
- Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.The Journal of chemical physics · 2016Article
- Internal coordinate molecular dynamics: a foundation for multiscale dynamics.The journal of physical chemistry. B · 2015Article
- GneimoSim: a modular internal coordinates molecular dynamics simulation package.Journal of computational chemistry · 2014Article
- Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement.PloS one · 2014Article
- Computational protein structure refinement: Almost there, yet still so far to go.Wiley interdisciplinary reviews. Computational molecular scienceArticle
- Kinase inhibitors allosterically disrupt a regulatory interaction to enhance PKCα membrane translocation.The Journal of biological chemistryArticle
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4 authors.
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Abstract
A longstanding challenge in using computational methods for protein structure prediction is the refinement of low-resolution structural models derived from comparative modeling methods into highly accurate atomistic models useful for detailed structural studies. Previously, we have developed and demonstrated the utility of the internal coordinate molecular dynamics (MD) technique, generalized Newton-Euler inverse mass operator (GNEIMO), for refinement of small proteins. Using GNEIMO, the high-frequency degrees of freedom are frozen and the protein is modeled as a collection of rigid clusters connected by torsional hinges. This physical model allows larger integration time steps and focuses the conformational search in the low frequency torsional degrees of freedom. Here, we have applied GNEIMO with temperature replica exchange to refine low-resolution protein models of 30 proteins taken from the continuous assessment of structure prediction (CASP) competition. We have shown that GNEIMO torsional MD method leads to refinement of up to 1.3 Å in the root-mean-square deviation in coordinates for 30 CASP target proteins without using any experimental data as restraints in performing the GNEIMO simulations. This is in contrast with the unconstrained all-atom Cartesian MD method performed under the same conditions, where refinement requires the use of restraints during the simulations.
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