Related papers: A new method for protein structure reconstruction …
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 tertiary structure defines its functions, classification and binding sites. Similar structural characteristics between two proteins often lead to the similar characteristics thereof. Determining structural similarity accurately in…
Traditional approaches to elucidation of protein structures by NMR spectroscopy rely on distance restraints also known as nuclear Overhauser effects (NOEs). The use of NOEs as the primary source of structure determination by NMR…
Understanding the structure of a protein complex is crucial indetermining its function. However, retrieving accurate 3D structures from microscopy images is highly challenging, particularly as many imaging modalities are two-dimensional.…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring…
Protein structure prediction has been a grand challenge problem in the structure biology over the last few decades. Protein quality assessment plays a very important role in protein structure prediction. In the paper, we propose a new…
Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of…
Despite the constant evolution of similarity searching research, it continues to face the same challenges stemming from the complexity of the data, such as the curse of dimensionality and computationally expensive distance functions.…
Recently developed deep learning techniques have significantly improved the accuracy of various speech and image recognition systems. In this paper we adapt some of these techniques for protein secondary structure prediction. We first train…
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…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
Current non-rigid structure from motion (NRSfM) algorithms are mainly limited with respect to: (i) the number of images, and (ii) the type of shape variability they can handle. This has hampered the practical utility of NRSfM for many…
Cryo-Electron Microscopy (cryo-EM) has emerged as a key technology to determine the structure of proteins, particularly large protein complexes and assemblies in recent years. A key challenge in cryo-EM data analysis is to automatically…
Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…
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…
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…
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…
Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for the investigation of three-dimensional structures of biological molecules such as proteins. Determining a protein structure is essential for understanding its function…