Related papers: Sparse approximations of protein structure from no…
Single-particle cryo-electron microscopy (cryo-EM) is a leading technology to resolve the structure of molecules. Early in the process, the user detects potential particle images in the raw data. Typically, there are many false detections…
Cryo-electron microscopy (cryo-EM) has become a tool of fundamental importance in structural biology, helping us understand the basic building blocks of life. The algorithmic challenge of cryo-EM is to jointly estimate the unknown 3D poses…
In the field of data mining, how to deal with high-dimensional data is an inevitable problem. Unsupervised feature selection has attracted more and more attention because it does not rely on labels. The performance of spectral-based…
We introduce the EMC algorithm for reconstructing a particle's 3D diffraction intensity from very many photon shot-noise limited 2D measurements, when the particle orientation in each measurement is unknown. The algorithm combines a…
Understanding protein flexibility and its dynamic interactions with other molecules is essential for studying protein function. Although cryogenic electron microscopy(cryo-EM) provides an opportunity to observe macromolecular dynamics…
Recent developments in deep learning-based methods demonstrated its potential to predict the 3D protein structures using inputs such as protein sequences, Cryo-Electron microscopy (Cryo-EM) images of proteins, etc. However, these methods…
Cryo-electron microscopy (cryo-EM) has revolutionized experimental protein structure determination. Despite advances in high resolution reconstruction, a majority of cryo-EM experiments provide either a single state of the studied…
The current state of the art in structural biology is led by NMR, X-ray crystallography and TEM investigations. These powerful tools however all rely on averaging over a large ensemble of molecules. Here, we present an alternative concept…
We apply two sparse reconstruction techniques, the least absolute shrinkage and selection operator (LASSO) and the sparse exponential mode analysis (SEMA), to two-dimensional (2D) spectroscopy. The algorithms are first tested on model data,…
Cryo-electron microscopy (cryo-EM) is capable of producing reconstructed 3D images of biomolecules at near-atomic resolution. As such, it represents one of the most promising imaging techniques in structural biology. However, raw cryo-EM…
A crucial step in single particle analysis (SPA) of cryogenic electron microscopy (Cryo-EM), 2D classification and alignment takes a collection of noisy particle images to infer orientations and group similar images together. Averaging…
Representation learning and \emph{de novo} generation of proteins are pivotal computational biology tasks. Whilst natural language processing (NLP) techniques have proven highly effective for protein sequence modelling, structure modelling…
In this paper, we present an algorithm for effectively reconstructing an object from a set of its tomographic projections without any knowledge of the viewing directions or any prior structural information, in the presence of pathological…
The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous structures derived from cryo-EM are now available in the…
Motivated by the structure reconstruction problem in single-particle cryo-electron microscopy, we consider the multi-target detection model, where multiple copies of a target signal occur at unknown locations in a long measurement, further…
In many branches of earth sciences, the problem of rock study on the micro-level arises. However, a significant number of representative samples is not always feasible. Thus the problem of the generation of samples with similar properties…
X-ray free-electron lasers (XFELs) offer unique capabilities for measuring the structure and dynamics of biomolecules, helping us understand the basic building blocks of life. Notably, high-repetition-rate XFELs enable single particle…
Unexpected structure in images of astronomical sources often presents itself upon visual inspection of the image, but such apparent structure may either correspond to true features in the source or be due to noise in the data. This paper…
Tailoring nanoparticles composition and morphology is of particular interest for improving their performance for catalysis. A challenge of this approach is that the nanoparticles optimized initial structure often changes during use.…
RFdiffusion is a popular and well-established model for generation of protein structures. However, this generative process offers limited insight into its internal representations and how they contribute to the final protein structure.…