Related papers: 3D Structure from 2D Microscopy images using Deep …
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…
In this work we set out to find a method to classify protein structures using a Deep Learning methodology. Our Artificial Intelligence has been trained to recognize complex biomolecule structures extrapolated from the Protein Data Bank…
Protein function is inherently linked to its localization within the cell, and fluorescent microscopy data is an indispensable resource for learning representations of proteins. Despite major developments in molecular representation…
Accurately modeling and designing protein complex structures is a central problem in computational structural biology, with broad implications for understanding cellular function and developing therapeutics. This thesis investigates two…
Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive,…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…
In this paper we address the problem of protein classification starting from a multi-view 2D representation of proteins. From each 3D protein structure, a large set of 2D projections is generated using the protein visualization software…
Cryo-Electron Microscopy (cryo-EM) has emerged as a key technology to determine the structure of proteins, particularly large protein complexes and assemblies in recent years. A key challenge in cryo-EM data analysis is to automatically…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
Learning on 3D structures of large biomolecules is emerging as a distinct area in machine learning, but there has yet to emerge a unifying network architecture that simultaneously leverages the graph-structured and geometric aspects of the…
Learning from 3D protein structures has gained wide interest in protein modeling and structural bioinformatics. Unfortunately, the number of available structures is orders of magnitude lower than the training data sizes commonly used in…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
Modeling the 3D structures of cells and tissues is crucial in biology. Sequential cross-sectional images from electron microscopy provide high-resolution intracellular structure information. The segmentation of complex cell structures…
The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the…
Cellular processes are governed by macromolecular complexes inside the cell. Study of the native structures of macromolecular complexes has been extremely difficult due to lack of data. With recent breakthroughs in Cellular electron cryo…
Despite the constant evolution of similarity searching research, it continues to face the same challenges stemming from the complexity of the data, such as the curse of dimensionality and computationally expensive distance functions.…
Understanding and extracting the patterns of microscopy images has been a major challenge in the biomedical field. Although trained scientists can locate the proteins of interest within a human cell, this procedure is not efficient and…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…