相关论文: On correlation between protein secondary structure…
In this work, which is the first of a series to prepare a cosmological parameter analysis with third-order cosmic shear statistics, we model both the shear three-point correlation functions $\Gamma^{(i)}$ and the third-order aperture…
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…
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
Based on overall 3D structure, proteins may be grouped into two broad categories, namely, globular proteins (spheroproteins), and elongated or rod-shaped proteins (RSP). The former comprises a significant majority of proteins. This work…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed…
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.…
We study the deposition of tetrahedral amorphous carbon (ta-C) films from molecular dynamics simulations based on a machine-learned interatomic potential trained from density-functional theory data. For the first time, the high $sp^3$…
Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions $\phi \approx 0.75$, a value that is similar to close packing equal-sized spheres. A limitation…
Deep learning has transformed protein design, enabling accurate structure prediction, sequence optimization, and de novo protein generation. Advances in single-chain protein structure prediction via AlphaFold2, RoseTTAFold, ESMFold, and…
In this study, we propose a Kernel-PCA model designed to capture structure-function relationships in a protein. This model also enables ranking of reaction coordinates according to their impact on protein properties. By leveraging machine…
We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by…
We discuss $\beta$-deformed geometries on two types of $T^3$'s where the direction along the third coordinate is not orthogonal to the direction along the second coordinate or the direction along the first coordinate. We show that the…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Using small angle neutron scattering, we conducted a detailed structural study of poly(3-alkylthiophenes) dispersed in deuterated dicholorbenzene. The focus was placed on addressing the influence of spatial arrangement of constituent atoms…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
Rigidity analysis using the "pebble game" has been applied to protein crystal structures to obtain information on protein folding, assembly and t he structure-function relationship. However, previous work using this technique has not made…
We study of the relation between the geometry of sets in complex hyperbolic space and Hilbert spaces with complete Pick kernels. We focus on the geometry associated with assembling sets into larger sets and of assembling Hilbert spaces into…