1. Autofocused 3D Classification of Cryoelectron Subtomograms
Yuxiang Chen, Stefan Pfeffer, José Jesús Fernández, Carlos Oscar S. Sorzano, Friedrich Förster 
Structure 
Volume 22, Issue 10, Pages (October 2014)
DOI: /j.str
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2. Structure 2014 22, 1528-1537DOI: (10.1016/j.str.2014.08.007)
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3. Figure 1 Main Methodological Features of AC3D
(A) Calculation of the focus masks FM1 and FM2 of two class centers V1 and V2.
(B) A voting strategy is used for multiclass label determination. The subtomogram under investigation with unknown class label (top left) will be assigned to the class with the most votes from pairwise comparisons, i.e., class 2 in this case.
(C) k-means++ is adapted as the initialization strategy. In the 2D simplification, each square represents a subtomogram. Assuming a subset of subtomograms (upper left, outlined with a solid line) is already chosen yielding the first class center (#1), the next class center (#2) is then the subtomogram average of a new subset (e.g., bottom right, outlined with a dashed line), in which each subtomogram is randomly picked with a probability proportional to the squared distance function (indicated by the colors of the squares and the scale bar).
Structure  , DOI: ( /j.str )
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4. Figure 2 Classification Result on Simulated Data Set of 80S Ribosomes
(A) Densities simulated from atomic models of three ribosome states. From left to right: S. cerevisiae 80S ribosome (model #1), 80S ribosome bound to the Sec61 translocon (model #2), and 80S ribosome bound to the SRP (model #3).
(B) Classification result. From left to right: subtomogram average of class #1, subtomogram average of class #2 colored by the STD against #1, and subtomogram average of class #3 colored by the STD against #1.
Structure  , DOI: ( /j.str )
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5. Figure 3
Classification Result for Mammalian Ribosomes Bound to the Native ER Protein Translocon
(A) The whole data set was first classified into 4 classes that apparently corresponded to the following assemblies: 80S ribosomes bound to a translocon population with only TRAP (class #1), 80S ribosomes bound to a translocon population with TRAP and OST (class #2), 60S ribosomes with only TRAP (class #3), and 60S ribosomes with TRAP and OST (class #4).
(B) Classes #1 and #2 were merged and further classified into three classes (C1, C2, and C3) with the focus on the ribosome density. The dotted circles mark the presence/absence of a nonribosomal density bound to the ribosomal stalk base, which likely corresponds to canonical translation elongation or termination factors. The three class averages are overlaid on the rightmost side to show the high flexibility of the ribosomal L1 stalk (outlined with a dotted rectangle).
(C) The FSC curves of the class averages in (B). For each class, three types of FSC curves are plotted: the intraclass FSC, the interclass FSC, and the FSC of a random portion with the same number of subtomograms.
Structure  , DOI: ( /j.str )
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