Related papers: Improvements of the REDCRAFT Software Package
Nuclear Magnetic Resonance (NMR) spectroscopy is one of the most powerful and widely used tools for molecular structure elucidation in organic chemistry. However, the interpretation of NMR spectra to determine unknown molecular structures…
Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep…
Monocular depth estimation is still an open challenge due to the ill-posed nature of the problem at hand. Deep learning based techniques have been extensively studied and proved capable of producing acceptable depth estimation accuracy even…
Three-dimensional (3D) reconstruction of trees has always been a key task in precision forestry management and research. Due to the complex branch morphological structure of trees themselves and the occlusions from tree stems, branches and…
We propose a novel neural architecture search algorithm via reinforcement learning by decoupling structure and operation search processes. Our approach samples candidate models from the multinomial distribution on the policy vectors defined…
With the rise of deep learning technology in practical applications, Convolutional Neural Networks (CNNs) have been able to assist humans in solving many real-world problems. To enhance the performance of CNNs, numerous network…
Classifying protein topology is essential for deciphering biological function, but progress is held back by the lack of large-scale benchmarks that avoid duplicates and by models that do not scale well. We introduce TEDBench, a large-scale,…
Deep learning based image segmentation methods have achieved great success, even having human-level accuracy in some applications. However, due to the black box nature of deep learning, the best method may fail in some situations. Thus…
We calculate the Inverse Beta Decay (IBD) antineutrino spectrum generated by nuclear reactors using the summation method to understand deviations from the smooth Huber-Mueller model due to the decay of individual fission products, showing…
The presence of gas pores in metal feedstock powder for additive manufacturing greatly affects the final AM product. Since current porosity analysis often involves lengthy X-ray computed tomography (XCT) scans with a full rotation around…
Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But,…
Encoder--decoder neural networks (EDNN) condense information most relevant to the output of the feedforward network to activation values at a bottleneck layer. We study the use of this architecture in emulation and interpretation of…
The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains…
Overfitted neural video codecs offer a decoding complexity orders of magnitude smaller than their autoencoder counterparts. Yet, this low complexity comes at the cost of limited compression efficiency, in part due to their difficulty…
There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality…
In single-particle cryo-electron microscopy (cryo-EM), the efficient determination of orientation parameters for 2D projection images poses a significant challenge yet is crucial for reconstructing 3D structures. This task is complicated by…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
Modern spectroscopic databases provide a wealth of information about the physical processes and environments associated with astrophysical populations. Techniques such as blind source separation (BSS), in which sets of spectra are…
Nuclear Magnetic Resonance (NMR) spectroscopy is a cornerstone technique for determining the structures of small molecules and is especially critical in the discovery of novel natural products and clinical therapeutics. Yet, interpreting…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…