Related papers: Soft disorder modulates the assembly path of prote…

Protein aggregation occurs when misfolded or unfolded proteins physically bind together, and can promote the development of various amyloid diseases. This study aimed to construct surrogate models for predicting protein aggregation via…

The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…

Hierarchically structured materials, which possess distinct features on different length scales, are ubiquitous in nature and engineering. In many cases, one structural level may be ordered while another structural level may be disordered.…

The self-assembly of particles into organized structures is a key feature of living organisms and a major engineering challenge. While it may proceed through the binding of perfectly matched, puzzle-pieces-like particles, many other…

Side chain flexibility is an important factor in ligand binding. In order to determine the extent to which side chain flexibility is involved in ligand binding, a knowledge-based approach was taken. A database composed of examples of…

Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…

Structural defects within amorphous packings of symmetric particles can be characterized using a machine learning approach that incorporates structure functions of radial distances and angular arrangement. This yields a scalar field,…

Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…

Structural prediction of protein-protein interactions is important to understand the molecular basis of cellular interactions, but it still faces major challenges when significant conformational changes are present. We propose a generative…

Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…

Studies of how protein fold have shown that the way protein clumps form in the test tube is similar to how proteins form the so-called ``amyloid'' deposits that are the pathological signal of a variety of diseases, among them the memory…

We employ molecular dynamics simulations to explore how internal flexibility affects phase transitions in soft-matter systems composed of dimers interacting via a core-softened potential with two characteristic length scales. Monomers are…

Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) interspersed between folded domains-are generally characterized as…

Designing protein-binding proteins with high affinity is critical in biomedical research and biotechnology. Despite recent advancements targeting specific proteins, the ability to create high-affinity binders for arbitrary protein targets…

Predicting the binding affinity of protein protein complexes directly from sequence remains a challenging problem, particularly in the absence of reliable structural information. Here I present ProtT Affinity, a sequence only model that…

Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of…

Motivation: Protein folding is a dynamic process during which a protein's amino acid sequence undergoes a series of 3-dimensional (3D) conformational changes en route to reaching a native 3D structure; the resulting 3D structural…

Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…

The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…

Geometric frustration offers a pathway to soft matter self-assembly with controllable finite sizes. While the understanding of frustration in soft matter assembly derives almost exclusively from continuum elastic descriptions, a current…