all the amino acids, estimate their pose and thread them into a protein chain in the 3D space. The density volume, obtained from 3D reconstruction of 2D microscope images, is represented as 3D matrices with continuous density value in each voxel. The sequential orders of amino acids, but not their locations, are known. Each amino acid can be represented by a class $C$ (20 types of standard amino acid), a 3D box and $N^C$ central locations of atoms in the amino acid. Each 3D box is parameterized by two coordinates: the front left top corner and the back right bottom corner. $N^C$ (4$\sim$14) is the number of the atoms in the amino acid, and it varies in different types.

$A^2$ Dataset
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As a benchmark for molecular structure determination, we built a large-scale Amino Acid ($A^2$) dataset of Cryo-EM density volumes. It contains 250,000 amino acids in 1713 simulated (by Chimera in 3 Å) electron density volumes and is annotated with rich information of amino acids. The amino acids are labeled with 3D boxes of 20 categories as well as the atomic coordinates. The amino acids in the dataset are dense, small objects that overlap each other, which makes the 