Related papers: Building Proteins in a Day: Efficient 3D Molecular…
We target the problem of estimating the center of mass of noisy 2-D images. We assume that the noise dominates the image, and thus many standard approaches are vulnerable to estimation errors. Our approach uses a surrogate function to the…
Cryo-electron tomography (cryoET) is a crucial technique for unveiling the structure of protein complexes. Automatically analyzing tomograms captured by cryoET is an essential step toward understanding cellular structures. In this paper, we…
Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…
In single particle reconstruction (SPR) from cryo-electron microscopy (cryo-EM), the 3D structure of a molecule needs to be determined from its 2D projection images taken at unknown viewing directions. Zvi Kam showed already in 1980 that…
Predicting the 3D structure of a macromolecule, such as a protein or an RNA molecule, is ranked top among the most difficult and attractive problems in bioinformatics and computational biology. Its importance comes from the relationship…
In 3-D reconstruction problems, the image data obtained from cryo electron microscopy is the projection of many heterogeneous instances of the object under study (e.g., a virus). When the object is heterogeneous but has an overall symmetry,…
We introduce a Bayesian genetic algorithm for reconstructing atomic models of nanoparticles from a single projection using Z-contrast imaging. The number of atoms in a projected atomic column obtained from annular dark field scanning…
In this report, we applied expectation and maximization (EM) method described by Philips et al [1] to recover two-dimensional (2D) structure from multiple sparse signal images in random orientation. The detailed derivation of EM algorithm…
Cryo-electron microscopy (cryo-EM) is unique among tools in structural biology in its ability to image large, dynamic protein complexes. Key to this ability is image processing algorithms for heterogeneous cryo-EM reconstruction, including…
Cryogenic electron microscopy (Cryo-EM) has become an essential tool for capturing high-resolution biological structures. Despite its advantage in visualizations, the large storage size of Cryo-EM data file poses significant challenges for…
Accurate determination of three-dimensional (3D) atomic structures is crucial for understanding and controlling the properties of nanomaterials. Atomic electron tomography (AET) offers non-destructive atomic imaging with picometer-level…
Knowing a biomolecule's structure is inherently linked to and a prerequisite for any detailed understanding of its function. Significant effort has gone into developing technologies for structural characterization. These technologies do not…
X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, and dual polarization interferometry, etc are indeed very powerful tools to determine the 3D structures of proteins (including the membrane proteins), though they are…
Protein complexes are macromolecules essential to the functioning and well-being of all living organisms. As the structure of a protein complex, in particular its region of interaction between multiple protein subunits (i.e., chains), has a…
This dissertation explores how deep generative models can advance the analysis of challenging biological problems by integrating domain knowledge with deep learning. It focuses on two areas: DNA reaction kinetics and cryogenic electron…
Cryo-electron microscopy (cryo-EM) has emerged as a powerful technique for determining the three-dimensional structures of biological molecules at near-atomic resolution. However, reconstructing helical assemblies presents unique challenges…
We introduce a framework for recovering an image from its rotationally and translationally invariant features based on autocorrelation analysis. This work is an instance of the multi-target detection statistical model, which is mainly used…
Macromolecules change their shape (conformation) in the process of carrying out their functions. The imaging by cryo-electron microscopy of rapidly-frozen, individual copies of macromolecules (single particles) is a powerful and general…
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and…
Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here, we developed a refinement protocol based on Gaussian mixture models that integrates particle…