Related papers: 3D Reconstruction of Protein Complex Structures Us…
Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
Predicting protein structure from the amino acid sequence has been a challenge with theoretical and practical significance in biophysics. Despite the recent progresses elicited by improved residue-residue contact prediction, contact-based…
A major challenge in single particle reconstruction methods using cryo-electron microscopy is to attain a resolution sufficient to interpret fine details in three-dimensional (3D) macromolecular structures. Obtaining high resolution 3D…
Cryo-electron microscopy (cryo-EM) remains pivotal in structural biology, yet the task of protein particle picking, integral for 3D protein structure construction, is laden with manual inefficiencies. While recent AI tools such as Topaz and…
Three-dimensional atomic force microscopy (3D-AFM) has been a powerful tool to probe the atomic-scale structure of solid-liquid interfaces. As a nanoprobe moves along the 3D volume of interfacial liquid, the probe-sample interaction force…
Image-based 3D reconstruction is one of the most important tasks in Computer Vision with many solutions proposed over the last few decades. The objective is to extract metric information i.e. the geometry of scene objects directly from…
Inverse rendering in a 3D format denoted to recovering the 3D properties of a scene given 2D input image(s) and is typically done using 3D Morphable Model (3DMM) based methods from single view images. These models formulate each face as a…
This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…
Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which…
Accurate thermal analysis of composites and porous media requires detailed characterization of local thermal properties in small scale. For some important applications such as lithium-ion batteries, changes in the properties during the…
Scanning probe experiments such as scanning tunneling microscopy (STM) and atomic force microscopy (AFM) on strongly correlated electronic systems often reveal complex pattern formation on multiple length scales. By studying the universal…
Designing novel proteins that bind to small molecules is a long-standing challenge in computational biology, with applications in developing catalysts, biosensors, and more. Current computational methods rely on the assumption that the…
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…
Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based…
Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with…
Cryo-EM is an increasingly popular method for determining the atomic resolution 3D structure of macromolecular complexes (eg, proteins) from noisy 2D images captured by an electron microscope. The computational task is to reconstruct the 3D…
Accurately predicting protein structures from amino acid sequences remains a fundamental challenge in computational biology, with profound implications for understanding biological functions and enabling structure-based drug discovery.…