ArticleJournal of molecular biology2013
PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment.
Article in Journal of molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Analyzing Fluctuation Properties in Protein Elastic Networks with Sequence-Specific and Distance-Dependent Interactions.Biomolecules · 2019Article
- Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank.Biophysical reviews · 2017Review
- Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.Acta crystallographica. Section D, Biological crystallography · 2015Article
- Aligning experimental and theoretical anisotropic B-factors: water models, normal-mode analysis methods, and metrics.The journal of physical chemistry. B · 2014Article
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2 authors.
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Abstract
In this study, a normal mode analysis, named phase integrated method (PIM), is developed for computing modes of biomolecules in a crystalline environment. PIM can calculate low-frequency modes on one or a few asymmetric units (AUs) and generate exact modes of a whole unit cell according to space group symmetry, while the translational symmetry between unit cells is maintained via the periodic boundary condition. Therefore, the method can dramatically reduce computational cost in mode calculation in the presence of crystal symmetry. PIM also has an option to map modes onto a single AU to form an orthonormalized mode set, which can be directly applied to normal-mode-based thermal parameter refinement in X-ray crystallography. The performance of PIM was tested on all 65 space groups available in protein crystals (one protein for each space group) and on another set of 83 ultra-high-resolution X-ray structures. The results showed that considering space group symmetry in mode calculation is crucial for accurately describing vibrational motion in a crystalline environment. Moreover, the optimal inter-AU packing stiffness was found to be about 60% of that of intra-AU interactions (non-bonded interaction only).
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