Related papers: Soft Matter Perspective on Protein Crystal Assembl…
Soft materials consist of basic units that are significantly larger than an atom but much smaller than the overall dimensions of the sample. The label "soft condensed matter" emphasizes that the large basic building blocks of these…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
As computers get faster, researchers -- not hardware or algorithms -- become the bottleneck in scientific discovery. Computational study of colloidal self-assembly is one area that is keenly affected: even after computers generate massive…
Organic molecular crystals are ideally placed to become next-generation piezoelectric materials due to their diverse chemistries that can be used to engineer tailor-made solid-state assemblies. Using crystal engineering principles, and…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD)…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an…
A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time by using a conventional relational…
From understanding the sand on the beach to the foam on your beer, soft sphere simulations have been crucial to the study of the amorphous world around us. However, many of the materials we interact with on a daily basis aren't comprised of…
Colloidal gels constitute an important class of materials found in many contexts and with a wide range of applications. Yet as matter far from equilibrium, gels exhibit a variety of time-dependent behaviours, which can be perplexing, such…
The complexity of condensed matter arises from emergent behaviors that cannot be understood by analyzing individual constituents in isolation. While traditional condensed-matter approaches-developed primarily for ideal crystalline…
Protein crystal production is a major bottleneck for the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy…
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…
Despite an artificial intelligence-assisted modeling of disordered crystals is a widely used and well-tried method of new materials design, the issues of its robustness, reliability, and stability are still not resolved and even not…
Conformational changes drive protein function, including catalysis, allostery, and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to…
While proteins have been treated as particles with a spherically symmetric interaction, of course in reality the situation is rather more complex. A simple step towards higher complexity is to treat the proteins as non--spherical particles…
A routine crystallography technique, crystal structure analysis, is rarely performed in computational condensed matter research. The lack of methods to identify and characterize crystal structures reliably in particle simulation data…
We adopt the point of view that analysis of the stability of the protein folding process is central to understanding the underlying physics of folding. Stability of the folding process means that many perturbations do not disrupt the…
The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical…
Efficient heuristics have predicted many functional materials such as high-temperature superconducting hydrides, while inorganic structural chemistry explains why and how the crystal structures are stabilized. Here we develop the paired…