Related papers: Improvements of the REDCRAFT Software Package
Nuclear Magnetic Resonance (NMR) spectroscopy leverages nuclear magnetization to probe molecules' chemical environment, structure, and dynamics, with applications spanning from pharmaceuticals to the petroleum industry. Despite its utility,…
A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…
Recent advances in protein structure prediction, such as AlphaFold, have demonstrated the power of deep neural architectures like the Evoformer for capturing complex spatial and evolutionary constraints on protein conformation. However, the…
Determining the interaction strength between proteins and small molecules is key to analyzing their biological function. Quantum-mechanical calculations such as \emph{Density Functional Theory} (DFT) give accurate and theoretically…
Accurate and efficient 3D reconstruction of trees is crucial for forest resource assessments and management. Close-Range Photogrammetry (CRP) is commonly used for reconstructing forest scenes but faces challenges like low efficiency and…
Photon-counting computed tomography (PCCT) has emerged as a promising imaging technique, enabling spectral imaging and material decomposition (MD). However, images typically suffer from a low signal-to-noise ratio (SNR) due to constraints…
Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
Structural pruning enables model acceleration by removing structurally-grouped parameters from neural networks. However, the parameter-grouping patterns vary widely across different models, making architecture-specific pruners, which rely…
A novel uracil-DNA degrading protein factor (termed UDE) was identified in Drosophila melanogaster with no significant structural and functional homology to other uracil-DNA binding or processing factors. Determination of the 3D structure…
Accurately assessing a patient's risk of a given event is essential in making informed treatment decisions. One approach is to stratify patients into two or more distinct risk groups with respect to a specific outcome using both clinical…
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…
Innovations like protein diffusion have enabled significant progress in de novo protein design, which is a vital topic in life science. These methods typically depend on protein structure encoders to model residue backbone frames, where…
Studies of one-body density matrices (ODM) are performed in various correlation methods, such as the Jastrow method, the correlated basis function method, the Green's function method and the generator coordinate method aiming to extract the…
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of proteins and other macromolecular complexes at near-atomic resolution. In single particle cryo-EM, the central problem is to reconstruct the…
Sequence specific resonance assignment and secondary structure determination of proteins form the basis for variety of structural and functional proteomics studies by NMR. In this context, an efficient standalone method for rapid assignment…
Overparameterized neural networks often contain many removable neurons, yet what makes a neuron redundant remains poorly understood. Existing pruning criteria commonly rely on local quantities such as weight magnitude, activation strength,…
Differentiating signals from the background in micrographs is a critical initial step for cryogenic electron microscopy (cryo-EM), yet it remains laborious due to low signal-to-noise ratio (SNR), the presence of contaminants and densely…
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…
Interactive molecular graphics applications facilitate analysis of three dimensional protein structures. Naturally, non-interactive 2-D snapshots of the protein structures do not convey the same level of geometric detail. Several 2-D…
The method of Probability Density Profile Analysis has been introduced previously as a tool to find the best match between a set of experimentally generated Residual Dipolar Couplings and a set of known protein structures. While it proved…