ArticleProceedings of the National Academy of Sciences of the United States of America2008
A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Measuring and modeling diffuse scattering in protein X-ray crystallography.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Ribosome Mechanics Informs about Mechanism.Journal of molecular biology · 2016Review
- PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment.Journal of molecular biology · 2013Article
- Coarse grained normal mode analysis vs. refined Gaussian Network Model for protein residue-level structural fluctuations.Bulletin of mathematical biology · 2013Article
- fSUB: normal mode analysis with flexible substructures.The journal of physical chemistry. B · 2012Article
- Physics-based de novo prediction of RNA 3D structures.The journal of physical chemistry. B · 2011Article
- Normal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic models.Archives of biochemistry and biophysics · 2011Article
- Anharmonic normal mode analysis of elastic network model improves the modeling of atomic fluctuations in protein crystal structures.Biophysical journal · 2010Article
- Temperature dependence of fluctuations in HIV1-protease.European biophysics journal : EBJ · 2010Article
- Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.Chemical reviews · 2010Review
- Global dynamics of proteins: bridging between structure and function.Annual review of biophysics · 2010Review
- A force field for virtual atom molecular mechanics of proteins.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model.Biophysical journal · 2009Article
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Authors and funding
2 authors.
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Abstract
In this article, we report a method for coarse-grained normal mode analysis called the minimalist network model. The main features of the method are that it can deliver accurate low-frequency modes on structures without undergoing initial energy minimization and that it also retains the details of molecular interactions. The method does not require any additional adjustable parameters after coarse graining and is computationally very fast. Tests on modeling the experimentally measured anisotropic displacement parameters in biomolecular x-ray crystallography demonstrate that the method can consistently perform better than other commonly used methods including our own one. We expect this method to be effective for applications such as structural refinement and conformational sampling.
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