Related papers: Improvements of the REDCRAFT Software Package
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…
One algorithm to predict protein structure is the residual dipolar coupling based residue assembly and filter tool (REDCRAFT). This algorithm exploits an exponential reduction of the search space of all possible structures to find a…
Residual Dipolar Couplings (RDCs) acquired by Nuclear Magnetic Resonance (NMR) spectroscopy can be an indispensable source of information in investigation of molecular structures and dynamics. Here we present a complete strategy for…
Computational protein structure determination involves optimization in a problem space much too large to exhaustively search. Existing approaches include optimization algorithms such as gradient descent and simulated annealing, but these…
We revisit the problem of protein structure determination from geometrical restraints from NMR, using convex optimization. It is well-known that the NP-hard distance geometry problem of determining atomic positions from pairwise distance…
The current paradigm for protein structure determination by NMR spectroscopy has thus far been based on collecting distance restrains between pairs of nuclei in the form of nuclear Overhauser enhancements (NOE). These, have in some…
Protein structure reconstruction from Nuclear Magnetic Resonance (NMR) experiments largely relies on computational algorithms. Recently, some effective low-rank matrix completion (MC) methods, such as ASD and ScaledASD, have been…
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…
Despite many advances in computational modeling of protein structures, these methods have not been widely utilized by experimental structural biologists. Two major obstacles are preventing the transition from a purely-experimental to a…
Despite the recent advances in various Structural Genomics Projects, a large gap remains between the number of sequenced and structurally characterized proteins. Some reasons for this discrepancy include technical difficulties, labor, and…
Protein inverse folding, the design of an amino acid sequence based on a target protein structure, is a fundamental problem of computational protein engineering. Existing methods either generate sequences without leveraging external…
Multidimensional NMR spectroscopy is one of the basic tools for determining the structure of biomolecules. Unfortunately, the resolution of the spectra is often limited by inter-nuclear couplings. This limitation cannot be overcome by…
The encoder-decoder networks are commonly used in medical image segmentation due to their remarkable performance in hierarchical feature fusion. However, the expanding path for feature decoding and spatial recovery does not consider the…
The nuclear-electronic orbital (NEO) method is a well-established approach for treating nuclei quantum mechanically in molecular systems beyond the usual Born-Oppenheimer approximation. In this work, we present a strategy to implement the…
Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…
Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce $\texttt{RecCrysFormer}$, a hybrid model that exploits the strengths of transformers with the aim of integrating…
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…
While accurate protein structure predictions are now available for nearly every observed protein sequence, predicted structures lack much of the functional context offered by experimental structure determination. We address this gap with…
Nuclear magnetic resonance (NMR) spectroscopy is one of the leading techniques for protein studies. The method features a number of properties, allowing to explain macromolecular interactions mechanistically and resolve structures with…
New soft- and hard decision decoding algorithms are presented for general Reed-Muller codes $\left\{\genfrac{}{}{0pt}{}{m}{r}\right\} $ of length $2^{m}$ and distance $2^{m-r}$. We use Plotkin $(u,u+v)$ construction and decompose code…