Related papers: Matching biomolecular structures by registration o…
The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal…
Understanding the structure of a protein complex is crucial indetermining its function. However, retrieving accurate 3D structures from microscopy images is highly challenging, particularly as many imaging modalities are two-dimensional.…
Upon a matrix representation of a binary bipartite network, via the permutation invariance, a coupling geometry is computed to approximate the minimum energy macrostate of a network's system. Such a macrostate is supposed to constitute the…
High-resolution 3D point clouds are highly effective for detecting subtle structural anomalies in industrial inspection. However, their dense and irregular nature imposes significant challenges, including high computational cost,…
Clustering is a technique for the analysis of datasets obtained by empirical studies in several disciplines with a major application for biomedical research. Essentially, clustering algorithms are executed by machines aiming at finding…
We can use a method called registration to integrate some point clouds that represent the shape of the real world. In this paper, we propose highly accurate and stable registration method. Our method detects keypoints from point clouds and…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Learning robust feature matching between the template and search area is crucial for 3D Siamese tracking. The core of Siamese feature matching is how to assign high feature similarity on the corresponding points between the template and…
Recently, cross-source point cloud registration from different sensors has become a significant research focus. However, traditional methods confront challenges due to the varying density and structure of cross-source point clouds. In order…
In this paper, we introduce a novel method for comparing 3D point clouds, a critical task in various machine learning applications. By interpreting point clouds as samples from underlying probability density functions, the statistical…
Single-particle electron cryomicroscopy (cryo-EM) is an increasingly popular technique for elucidating the three-dimensional structure of proteins and other biologically significant complexes at near-atomic resolution. It is an imaging…
Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of…
Feature descriptors of point clouds are used in several applications, such as registration and part segmentation of 3D point clouds. Learning discriminative representations of local geometric features is unquestionably the most important…
The paper investigates the problem of fitting protein complexes into electron density maps. They are represented by high-resolution cryoEM density maps converted into overlapping matrices and partly show a structure of a complex. The…
When applying automatic analysis of fluorescence or histopathological images of cells, it is necessary to partition, or de-clump, partially overlapping cell nuclei. In this work, I describe a method of partitioning partially overlapping…
While several feature embedding models have been developed in the literature, comparisons of these embeddings have largely focused on their numerical performance in classification-related downstream applications. However, an interpretable…
We consider the point cloud registration problem, the task of finding a transformation between two point clouds that represent the same object but are expressed in different coordinate systems. Our approach is not based on a point-to-point…
Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. CryoEM provides direct visualization of individual macromolecules sampling different conformational and compositional states.…
Many clustering problems in computer vision and other contexts are also classification problems, where each cluster shares a meaningful label. Subspace clustering algorithms in particular are often applied to problems that fit this…
Structural assessment of biomolecular complexes is vital for translating molecular models into functional insights, shaping our understanding of biology and aiding drug discovery. However, current structure-based scoring functions often…