Journal Article10.1126/SCIENCE.1110428
Inferential Structure Determination
TL;DR: This work used Bayesian inference to derive a probability distribution that represents the unknown structure and its precision and implemented this approach by using Markov chain Monte Carlo techniques, providing an objective figure of merit and improves structural quality.
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Abstract: Macromolecular structures calculated from nuclear magnetic resonance data are not fully determined by experimental data but depend on subjective choices in data treatment and parameter settings. This makes it difficult to objectively judge the precision of the structures. We used Bayesian inference to derive a probability distribution that represents the unknown structure and its precision. This probability distribution also determines additional unknowns, such as theory parameters, that previously had to be chosen empirically. We implemented this approach by using Markov chain Monte Carlo techniques. Our method provides an objective figure of merit and improves structural quality.
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Citations
A Bayesian view on cryo-EM structure determination.
TL;DR: A Bayesian interpretation of cryo-EM structure determination is described, where smoothness in the reconstructed density is imposed through a Gaussian prior in the Fourier domain, so that the optimal 3D linear filter is obtained without the need for arbitrariness and objective resolution estimates may be obtained.
962
Outcome of the First Electron Microscopy Validation Task Force Meeting
Richard Henderson,Andrej Sali,Matthew L. Baker,Bridget Carragher,Batsal Devkota,Kenneth H. Downing,Edward H. Egelman,Zukang Feng,Joachim Frank,Joachim Frank,Nikolaus Grigorieff,Wen Jiang,Steven J. Ludtke,Ohad Medalia,Pawel A. Penczek,Peter B. Rosenthal,Michael G. Rossmann,Michael F. Schmid,Gunnar F. Schröder,Alasdair C. Steven,David L. Stokes,John D. Westbrook,Willy Wriggers,Huanwang Yang,Jasmine Young,Helen M. Berman,Wah Chiu,Gerard J. Kleywegt,Catherine L. Lawson +28 more
TL;DR: This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Validation Task Force organized by the Unified Data Resource for 3DEM and aims to increase the impact of 3DEM in biology and medicine.
556
Structure of the human voltage-dependent anion channel
Monika Bayrhuber,Thomas Meins,Michael Habeck,Stefan Becker,Karin Giller,Saskia Villinger,Clemens Vonrhein,Christian Griesinger,Markus Zweckstetter,Kornelius Zeth +9 more
TL;DR: The 3D structure of human VDAC1 was solved conjointly by NMR spectroscopy and x-ray crystallography in this paper, which is the most abundant protein in the mitochondrial outer membrane (MOM).
The molecular sociology of the cell
TL;DR: Using emerging experimental techniques, such as mass spectrometry of complexes and single-particle cryo-electron microscopy, to complement traditional biochemical and biophysical methods will uncover the molecular architectures, and perhaps even atomic models, of many protein complexes.
540
High-resolution structure prediction and the crystallographic phase problem
TL;DR: The results suggest that the combination of high-resolution structure prediction with state-of-the-art phasing tools may be unexpectedly powerful in phasing crystallographic data for which molecular replacement is hindered by the absence of sufficiently accurate previous models.
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IL-13受体α2降低血吸虫病肉芽肿的炎症反应并延长宿主存活时间[英]/Mentink-Kane MM,Cheever AW，Thompson RW，et al//Proc Natl Acad Sci U S A
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Hybrid Monte Carlo
TL;DR: In this article, a hybrid (molecular dynamics/Langevin) algorithm is used to guide a Monte Carlo simulation of lattice field theory, which is especially efficient for quantum chromodynamics which contain fermionic degrees of freedom.
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