Related papers: A new method for protein structure reconstruction …
Proteins are essential for maintaining life. For example, knowing the structure of a protein, cell regulatory mechanisms of organisms can be modeled, supporting the development of disease treatments or the understanding of relationships…
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,…
Localizing a cloud of points from noisy measurements of a subset of pairwise distances has applications in various areas, such as sensor network localization and reconstruction of protein conformations from NMR measurements. In [1], Drineas…
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…
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it…
The ability to reconstruct high-quality images from undersampled MRI data is vital in improving MRI temporal resolution and reducing acquisition times. Deep learning methods have been proposed for this task, but the lack of verified methods…
Due to the advancements in technology number of entries in the structural database of proteins are increasing day by day. Methods for retrieving protein tertiary structures from this large database is the key to comparative analysis of…
Single-particle electron microscopy is a modern technique that biophysicists employ to learn the structure of proteins. It yields data that consist of noisy random projections of the protein structure in random directions, with the added…
The comparison of protein structures is a fundamental task in computational biology, crucial for understanding protein function, evolution, and for drug design. While analytical methods like the Kabsch algorithm provide an exact,…
Recent advancements in deep learning for predicting 3D protein structures have shown promise, particularly when leveraging inputs like protein sequences and Cryo-Electron microscopy (Cryo-EM) images. However, these techniques often fall…
Discovering the 3D atomic structure of molecules such as proteins and viruses is a fundamental research problem in biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising vision-based technique for structure estimation which…
The Euclidean distance geometry problem arises in a wide variety of applications, from determining molecular conformations in computational chemistry to localization in sensor networks. When the distance information is incomplete, the…
Protein structure similarity search (PSSS), which tries to search proteins with similar structures, plays a crucial role across diverse domains from drug design to protein function prediction and molecular evolution. Traditional…
Coarse-grained models can be of great help to address the problem of structure prediction in nucleic acids. On one hand they can make the prediction more efficient, while on the other hand, they can also help to identify the essential…
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…
Protein structure determination has long been one of the primary challenges of structural biology, to which deep machine learning (ML)-based approaches have increasingly been applied. However, these ML models generally do not incorporate…
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…
Traditional approaches to elucidation of protein structures by NMR spectroscopy rely on distance restraints also know as nuclear Overhauser effects (NOEs). The use of NOEs as the primary source of structure determination by NMR spectroscopy…
Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale,…
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…