Related papers: A New Route for the Determination of Protein Struc…
We study the local distortion of the atomic structure in small biological samples illuminated by x-ray free electron laser (XFEL) pulses. We concentrate on the effect of inhomogenities: heavy atoms in a light matrix and non-homogeneous…
Experimentally obtained X-ray diffraction (XRD) patterns can be difficult to solve, precluding the full characterization of materials, pharmaceuticals, and geological compounds. Herein, we propose a method based upon a multi-objective…
Proteins carry out biological functions through the coordinated action of groups of residues organized into structural arrangements. These arrangements, which we refer to as protein units, exist at an intermediate scale, being larger than…
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…
Under prolonged starvation, the nucleoid of E. coli bacteria forms nanocrystalline complexes with the protein Dps. By one hypothesis, this effect is considered to be a manifestation of a general strategy of self-preservation of living…
Predicting the 3D structure of a macromolecule, such as a protein or an RNA molecule, is ranked top among the most difficult and attractive problems in bioinformatics and computational biology. Its importance comes from the relationship…
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…
The European X-ray Free Electron Laser (XFEL.EU) will provide unprecedented peak brilliance and ultra-short and spatially coherent X-ray pulses in an energy range of 0.25 to 25 keV . The pulse timing structure is unique with a burst of 2700…
A fundamental challenge in protein design is the trade-off between generating structural diversity while preserving motif biological function. Current state-of-the-art methods, such as partial diffusion in RFdiffusion, often fail to resolve…
Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. Methods…
Proteins are macromolecules responsible for essential functions in almost all living organisms. Designing reasonable proteins with desired functions is crucial. A protein's sequence and structure are strongly correlated and they together…
Most material discrimination in security inspections is based on dual-energy x-ray imaging, which enables the determination of a material's effective atomic number (Zeff) as well as electron density and its consequent classification as…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal…
The European X-ray Free Electron Laser (XFEL) will deliver 30,000 fully coherent, high brilliance X-ray pulses per second each with a duration below 100 fs. This will allow the recording of diffraction patterns of single complex molecules…
Recently, deep convolutional neural networks have shown good results for image recognition. In this paper, we use convolutional neural networks with a finder module, which discovers the important region for recognition and extracts that…
Models such as AlphaFold2 and OpenFold have transformed protein structure prediction, yet their inner workings remain poorly understood. We present a methodology to systematically evaluate the contribution of individual OpenFold components…
Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter…
Construction of a scaffold structure that supports a desired motif, conferring protein function, shows promise for the design of vaccines and enzymes. But a general solution to this motif-scaffolding problem remains open. Current…
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…