More and more deep learning approaches have been proposed to segment secondary structures from cryo-electron density maps at medium resolution range (5--10Å). Although the deep learning approaches show great potential, only a few small experimental ...

Although Cryo-electron microscopy (cryo-EM) has been successfully used to derive atomic structures for many proteins, it is still challenging to derive atomic structure when the resolution of cryo-EM density maps is in the medium range, e.g., 5-10 Å. ...

Cryo-electron microscopy is a major structure determination technique for large molecular machines and membrane-associated complexes. Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current ...

Small heat shock proteins (sHSP) are molecular chaperons which play a key role in protein homeostasis under stress conditions. Point mutation of aspartic acid (D) substitution for asparagine (N) at residue 11 (D11N) in HSP16.9B protein was predicted in ...

Electron cryo-microscopy (Cryo-EM) technique produces density maps that are 3-dimensional (3D) images of molecules. It is challenging to derive atomic structures of proteins from 3D images of medium resolutions. Twist of a α-strand has been studied ...

Cryo-electron microscopy (Cryo-EM) has become central to the study of large-scale molecular interactions and has produced three-dimensional (3D) density maps at various resolutions. Secondary structure element (SSE) identification from volumetric ...

Searching genomes to locate noncoding RNA genes with known secondary structure is an important problem in bioinformatics. In general, the secondary structure of a searched noncoding RNA is defined with a structure model constructed from the structural ...

Cryo-Electron Microscopy is a biophysical technique that generates volumetric images of macromolecules. Although it is hard to distinguish the backbone from the density map at medium resolutions such as 5-10Å, the location of major secondary structure ...

A β-sheet is composed of multiple β-strands that are stabilized by inter-strand hydrogen bonds. It has been discovered that a β-sheet is right-handed twisted. We have developed a geometrical method to investigate the relationship between the twist of a ...

Efficient DFB broad-area lasers enable spectrally-resolved measurements of lateral field profiles to high powers, indicating brightness is limited by both increasing numbers of guided modes and degradation of beam quality of low order modes.

Electron cryomicroscopy is becoming a major experimental technique in solving the structures of large molecular assemblies. More and more three-dimensional images have been obtained at the medium resolutions between 5 and 10Å. At this resolution range, ...

Secondary structure element (SSE) identification from volumetric protein density maps is critical for de-novo backbone structure derivation in electron cryo-microscopy (cryoEM). Although multiple methods have been developed to detect SSE from the ...

Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies. The prohibitive sizes of the mutational and ...

Structural studies of proteins for motif mining and other pattern recognition techniques require the abstraction of the structure into simpler elements for robust matching. In this study, we propose the use of bond-orientational order parameters, a well-...

Although many tools were developed for visualization of RNA secondary structure, RNA-DV is a tool which provides a flexible and powerful interface for RNA secondary structure design and visualization. Being able to dynamically make modification and ...

Cryo-electron Microscopy (cryoEM) is an advanced imaging technique that produces volume maps at different resolutions. This technique is capable of visualizing large molecular complexes such as viruses and ribosomes. At the medium resolutions, such as 5 ...

Determination of binding sites between proteins has a wide range of applications. Understanding energetics and mechanism of complexes remains one of the essential problems in binding site prediction. We develop a system, P-Binder, for identifying ...

To identify splice sites more accurately and efficiently, a method for the recognition of splice sites based on comprehensive information is proposed. By analyzing the splicing signals, splicing sequences, secondary structures of flank sequence, ...

The desire to start evolution from scratch inside a computer memory is as old as computing. Here we demonstrate how viable computer programs can be established de novo in a Precambrian environment without supplying any specific instantiation, just ...

The identification of RNA secondary structures has been among the most exciting recent developments in biology and medical science. It has been recognized that there is an abundance of functional structures with frameshifting, regulation of translation, ...