The Spike (S) protein of the SARS-CoV-2 virus that causes the COVID-19 disease is considered the most important target for vaccine, drug and therapeutic research as it attaches and binds to the ACE2 receptor of the host cells and allows the entry of...
Fluorine is a common substituent in medicinal chemistry and is found in up to 50% of the most profitable drugs. In this study, a statistical analysis of the nature, geometry, and frequency of hydrogen bonds (HBs) formed between the aromatic and aliph...
Parkinson’s disease is an idiopathic neurodegenerative disorder which is characterized by the degeneration of the neurons of substantia nigra, a part of the midbrain, regulating motor movement. It involves a decrease in the levels of dopamine w...
SARS-CoV-2, the virus responsible for coronavirus disease COVID-19, is a highly transmissible pathogen that has caused substantial global morbidity and mortality. The ongoing COVID-19 pandemic caused by this virus has had a significant impact on publ...
The physicochemical properties of amino acid residues from the AAindex database are widely used as predictors in building models for predicting both protein structures and properties. It should be noted, however, that the AAindex database contains da...
The structural determination and characterization of molecules, namely proteins and enzymes, is crucial to gaining a better understanding of their role in different chemical and biological processes. The continuous technical developments in the exper...
Proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the Protein Data Bank (PDB). Our analysis of recent PDB data revealed that only 42.53% of PDB entries (1...
The number of available protein structures in the Protein Data Bank (PDB) has considerably increased in recent years. Thanks to the growth of structures and complexes, numerous large-scale studies have been done in various research areas, e.g., prote...
11 September 2025
We have evaluated the quality of all 325 deposits in the PDB (as of December 2024) that correspond to (or contain) the catalytic domain of cAMP-dependent protein kinases (PKA). Detailed analysis was possible for 289 deposits of crystal structures tha...
A systematic evaluation of the CSD and the PDB in conjunction with DFT calculations reveal that non-covalent Carbon-bonding interactions with X–CH3 can be weakly directional in the solid state (P ≤ 1.5) when X = N or O. This is comparable to...
The crystallized ligands in the Protein Data Bank (PDB) can be treated as the inverse shapes of the active sites of corresponding proteins. Therefore, the shape similarity between a molecule and PDB ligands indicated the possibility of the molecule t...
In this paper, we present an update to the ellipsoid profile algorithm (EP), a simple technique for the measurement of the globularity of protein structures without the calculation of molecular surfaces. The globularity property is understood in this...
As the number of macromolecular structures in the worldwide Protein Data Bank (wwPDB) continues to grow rapidly, more attention is being paid to the quality of its data, especially for use in aggregated structural and dynamics analyses. In this study...
Parkinson’s disease is a neurodegenerative disease which involves the malfunction and death of vital nerve cells in the brain, called neurons, which produce dopamine. Dopamine is a neurotransmitter that communicates with the area of the brain r...
An improved P-type doped barrier surface AlGaN/GaN high electron mobility transistor with high power-added efficiency (PDBS-HEMT) is proposed in this paper. Through the modelling and simulation of ISE-TCAD and ADS software, the influence of the P-typ...
The morphology and secondary metabolism of Aspergillus spp. are associated with initial spore density (ISD). Fatty acids (FA) are involved in the biosynthesis of aflatoxins (AF) through Aspergillus quorum sensing (QS). Here, we studied how ochratoxin...
Complications of diabetes mellitus (DM) range from acute to chronic conditions, leading to multiorgan disorders such as nephropathy, retinopathy, and neuropathy. However, little is known about the influence of DM on intervertebral disc degeneration (...
This study quantifies how confinement changes the orientational phase space of proteins by comparing hanging-drop (HD) with Langmuir–Blodgett (LB) conditions within a unified probabilistic framework grounded in structural data from the Protein...
A fungal isolate Aspergillus terreus PDB-B (accession number: MT774567.1), which could tolerate up to 500 mg/L of cypermethrin, was isolated from the lake sediments of Kulamangalam tropical lake, Madurai, and identified by internal transcribed spacer...
In this manuscript, we combine high-level ab initio calculations on some model systems (XCH3 σ-hole/H-bond donors) and a Protein Data Bank (PDB) survey to distinguish between trifurcated H-bonds and noncovalent carbon bonds in XCH3···O complexes (X =...
The future development of communication systems will create a great demand for the internet of things (IOT), where the overall control of all IOT nodes will become an important problem. Considering the essential issues of miniaturization and energy c...
Carboxylic ester hydrolases (CEHs), which catalyze the hydrolysis of carboxylic esters to produce alcohol and acid, are identified in three domains of life. In the Protein Data Bank (PDB), 136 crystal structures of bacterial CEHs (424 PDB codes) from...
Protein structure analysis is essential in various bioinformatics domains such as drug discovery, disease diagnosis, and evolutionary studies. Within structural biology, the classification of protein structures is pivotal, employing machine learning...
Coronavirus disease (SARS-CoV-2) is a global epidemic. This pandemic, which has been linked to high rates of death, has forced some countries throughout the world to implement complete lockdowns in order to contain the spread of infection. Because of...
MSALigMap (Multiple Sequence Alignment Ligand Mapping) is a tool for mapping active-site amino-acid residues that bind selected ligands on to target protein sequences of interest. Users can also provide novel sequences (unavailable in public database...
In this work, intra- and intermolecular halogen and chalcogen bonds (HlgBs and ChBs, respectively) present in the solid state of nucleic acids (NAs) have been studied at the RI-MP2/def2-TZVP level of theory. To achieve this, a Protein Data Bank (PDB)...
An understanding of the functional mechanisms of G-protein-coupled receptors (GPCRs) is very important for GPCR-related drug design. We have developed an integrated GPCR database (SEVENS http://sevens.cbrc.jp/) that includes 64,090 reliable GPCR gene...
Crystallography plays a crucial role in understanding the functions of macromolecules by determining their three-dimensional structures at the atomic level. This review outlines the history of crystallization, explains the principles of crystallizati...
We explored the pharmacology of the P-glycoprotein (P-gp) efflux pump and its role in multidrug resistance. We used Protein Data Bank (PDB) database mining and the artificial intelligence (AI) model Boltz-2.1.1, developed for simultaneous structure a...
Our understanding of the structure–function relationships of biomolecules and thereby applying it to drug discovery programs are substantially dependent on the availability of the structural information of ligand–protein complexes. However, the corre...
The presence of protein structures with atypical folds in the Protein Data Bank (PDB) is rare and may result from naturally occurring knots or crystallographic errors. Proper characterisation of such folds is imperative to understanding the basis of...
ERF family transcription factors are crucial regulators in plants, playing a central role in abiotic stress responses and serving as important targets for stress-tolerant crop breeding. Populus davidiana × P. bolleana, an elite hybrid poplar cu...
Drought stress is a common adverse environment that plants encounter, and many drought-tolerant genes have been characterized. The gene regulatory network (GRN) is important in revealing the drought tolerance mechanism. Here, to investigate the regul...
The number of databases of natural products (NPs) has increased substantially. Latin America is extraordinarily rich in biodiversity, enabling the identification of novel NPs, which has encouraged both the development of databases and the implementat...
Recently, a distribution management system (DMS) that can conduct periodical system analysis and control by mounting various applications programs has been actively developed. In this paper, we summarize the development and demonstration of a databas...
The effect of the temperature and salt solution on the structural characteristics of the protein 1BBL was investigated by molecular dynamics simulations. The paper presents simulation results regarding the non-bonded energy and the structural stabili...
Boron presents an important role in chemistry, biology, and materials science. Diatomic transition-metal borides (MBs) are the building blocks of many complexes and materials, and they present unique electronic structures with interesting and peculia...
Ultrathin Pd/B4C multilayers are suitable X-ray mirrors working at the photon energy region of 7–20 keV. To further improve the layer structure, Pd/B4C multilayers with a d-spacing of 2.5 nm were fabricated by magnetron sputtering using the hea...
Introduction: The DEAF1 (Deformed Epidermal Autoregulatory Factor 1) gene is a highly expressed transcription factor in the central nervous system and is essential for embryonic and neuronal development [...]
Pd/B4C multilayers with 2.5 nm of d-spacing and thick Si and B4C capping layers were fabricated to study temporal stability under storage in different environments with relative humidity of 10% and 50%. The two stored samples were investigated using...
Thirty years ago a class of proteins was found to prevent the aggregation of Rubisco. These proteins’ ability to prevent unwanted associations led to their being called chaperones. These chaperone proteins also increased in expression as a resp...
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and manag...
In this study, the yak’s TLR4 gene alternative spliceosomes were investigated using PCR amplification and cloning to improve disease-resistance in yak and promote efficient utilization of yak’s resources. qRT-PCR was used to determine the...
It has long been understood that some proteins undergo conformational transitions en route to the Michaelis Complex to allow chemistry. Examination of crystal structures of glycosyltransferase enzymes in the GT-B structural class reveals that the pre...
The G-quadruplex DNA structures are mainly present at the terminal portion of telomeres and can be stabilized by ligands able to recognize them in a specific manner. The recognition process is usually related to the inhibition of the enzyme telomeras...
Intrinsically-disordered regions lack a well-defined 3D structure, but play key roles in determining the function of many proteins. Although predictors of disorder have been shown to achieve relatively high rates of correct classification of these se...
Cholecystokinin 1 receptor (CCK1R) is activated by singlet oxygen (1O2) in type II photodynamic action in isolated rat, mouse, and Peking duck pancreatic acini. To examine whether this is maintained outside the microenvironment of pancreatic acinar c...
Protein–ligand complexes in crystal structures are well described by an array of bonding interactions among precisely defined functional groups. The present work examines how one representative complex behaves in one-microsecond molecular dynam...
Silkworm Bombyx mori is an economically important insect and a lepidopteran model. Organelle proteome is vital to understanding gene functions; however, it remains to be identified in silkworm. Here, using the engineered ascorbate peroxidase APEX, we...
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data B...
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