ArticleProteins2009
Comparisons of experimental and computed protein anisotropic temperature factors.
Article in Proteins, 2009. 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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13 citing papers in PubMed, 42 citations in OpenAlex.
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- Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes.International journal of molecular sciences · 2021Article
- Analyzing Fluctuation Properties in Protein Elastic Networks with Sequence-Specific and Distance-Dependent Interactions.Biomolecules · 2019Article
- Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.Acta crystallographica. Section F, Structural biology communications · 2019Review
- Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank.Biophysical reviews · 2017Review
- Dynamical persistence of active sites identified in maltose-binding protein.Journal of molecular modeling · 2017Article
- Molecular dynamics simulation of triclinic lysozyme in a crystal lattice.Protein science : a publication of the Protein Society · 2016Article
- Molecular Dynamics Assisted Mechanistic Study of Isoniazid-Resistance against Mycobacterium tuberculosis InhA.PloS one · 2015Article
- Computational and experimental characterization of RNA cubic nanoscaffolds.Methods (San Diego, Calif.) · 2014Article
- Aligning experimental and theoretical anisotropic B-factors: water models, normal-mode analysis methods, and metrics.The journal of physical chemistry. B · 2014Article
- Anharmonic normal mode analysis of elastic network model improves the modeling of atomic fluctuations in protein crystal structures.Biophysical journal · 2010Article
- Protein elastic network models and the ranges of cooperativity.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Prediction of methionine oxidation risk in monoclonal antibodies using a machine learning method.mAbsArticle
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Because of its appealing simplicity, the anisotropic network model (ANM) has been widely accepted and applied to study many molecular motion problems: such as ribosome motions, the molecular mechanisms of GroEL-GroES function, allosteric changes in hemoglobin, motor-protein motions, and conformational changes in general. However, the validity of the ANM has not been closely examined. In this work, we use ANM to predict the anisotropic temperature factors of proteins obtained from X-ray and NMR data. The rich, directional anisotropic temperature factor data available for hundreds of proteins in the protein data bank are used as validation data to closely test the ANM model. The significance of this work is that it presents a timely, important evaluation of the model, shows the extent of its accuracy in reproducing experimental anisotropic temperature factors, and suggests ways to improve the model. An improved model will help us better understand the internal dynamics of proteins, which in turn can greatly expand the usefulness of the models, which has already been demonstrated in many applications.
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