RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data

The Partial Derivative Method for Dynamic Stiffness and Damping Coefficients of Supercritical CO2 Foil Bearings

Supercritical CO2 foil bearings are promising bearing technology for supercritical CO2 high-speed turbomachinery. The partial derivative method including complete variable perturbation of the compressible turbulent lubrication Reynolds equation is effective to predict the frequency dependent dynamic stiffness and damping coefficients of supercritical CO2 bearings. In this research, the structural perturbation of foil dynamic model was introduced into this method and then the dynamic coefficients of supercritical CO2 foil bearings were calculated. The results of parametric analysis show that the structural loss factor has little influence on the trend of dynamic coefficients changing with the dimensionless support stiffness but mainly affects the value of stiffness coefficients as well as damping coefficients. Due to the turbulence effect, the bearing number is not able to directly determine the characteristics of supercritical CO2 foil bearings, which is different from air bearings. Compared to the bearing number, the influence of the average Reynolds number on the change of dynamic coefficients with dimensionless support stiffness is more obvious

The Partial Derivative Method for Dynamic Stiffness and Damping Coefficients of Supercritical CO₂ Foil Bearings

Supercritical CO2 foil bearings are promising bearing technology for supercritical CO2 high-speed turbomachinery. The partial derivative method including complete variable perturbation of the compressible turbulent lubrication Reynolds equation is effective to predict the frequency dependent dynamic stiffness and damping coefficients of supercritical CO2 bearings. In this research, the structural perturbation of foil dynamic model was introduced into this method and then the dynamic coefficients of supercritical CO2 foil bearings were calculated. The results of parametric analysis show that the structural loss factor has little influence on the trend of dynamic coefficients changing with the dimensionless support stiffness but mainly affects the value of stiffness coefficients as well as damping coefficients. Due to the turbulence effect, the bearing number is not able to directly determine the characteristics of supercritical CO2 foil bearings, which is different from air bearings. Compared to the bearing number, the influence of the average Reynolds number on the change of dynamic coefficients with dimensionless support stiffness is more obvious

Dynamic Coefficients of Tilting Pad Bearing by Perturbing the Turbulence Model

Tilting pad bearings are appropriate for the trend of high efficiency and reliability design of rotating machinery due to their high stability. The laminar and turbulent flow states exist in the lubricating oil film of high-speed and heavy-load tilting pad bearings simultaneously. By perturbing the multiple flow state lubrication model with a partial derivative method, together with the pad-pivot structural perturbations, the frequency-dependent stiffness and damping coefficients of tilting pad bearings, embracing the effect of dynamical variations of both turbulence and pressure-viscous, were numerically solved in this research. The importance of each perturbed variable was studied, and the results indicate that the perturbed film thickness included in turbulence coefficients perturbations is significant enough to be taken into account otherwise the equivalent stiffness coefficients will be obviously overestimated. Unlike the perturbed film thickness, the consideration of the perturbed viscosity is optional, because it makes the stiffness and damping coefficients larger at both laminar and turbulent flow states. For a simplified simulation and conservative prediction results, the perturbed viscosity can be neglected

Dynamic Coefficients of Tilting Pad Bearing by Perturbing the Turbulence Model

Tilting pad bearings are appropriate for the trend of high efficiency and reliability design of rotating machinery due to their high stability. The laminar and turbulent flow states exist in the lubricating oil film of high-speed and heavy-load tilting pad bearings simultaneously. By perturbing the multiple flow state lubrication model with a partial derivative method, together with the pad-pivot structural perturbations, the frequency-dependent stiffness and damping coefficients of tilting pad bearings, embracing the effect of dynamical variations of both turbulence and pressure-viscous, were numerically solved in this research. The importance of each perturbed variable was studied, and the results indicate that the perturbed film thickness included in turbulence coefficients perturbations is significant enough to be taken into account otherwise the equivalent stiffness coefficients will be obviously overestimated. Unlike the perturbed film thickness, the consideration of the perturbed viscosity is optional, because it makes the stiffness and damping coefficients larger at both laminar and turbulent flow states. For a simplified simulation and conservative prediction results, the perturbed viscosity can be neglected

Fantasy curiosity:a new theoretical perspective to understand anime pilgrimage

Curiosity stands as a significant driving force in comprehending tourist behaviour. Nonetheless, within the realm of anime pilgrims, the objects of interest, the underlying mechanisms and the resulting behaviours stemming from their curiosity deviate notably from those exhibited by typical tourists. Through the utilization of in-depth case studies of anime pilgrims, this research unveils an innovative impetus for tourism known as ‘fantasy curiosity’ with four distinct attributes, differentiating it from prevailing conceptualizations of general curiosity. Moreover, by utilizing a Latent Dirichlet Allocation model, we pinpoint distinct characteristics of anime-related behaviours across different phases of anime tours. These findings serve to propel the progression of research within the realms of tourism motivations, while concurrently broadening the horizons of curiosity theory.</p

A UFLC/MS/MS method for simultaneous quantitation of alisol A and alisol B 23-acetate from Alisma orientale (Sam.) Juz. in rat plasma

A sensitive and reliable ultra fast liquid chromatography tandem mass spectrometry (UFLC-MS/MS) method has been developed and validated for simultaneous quantitation of alisol A and alisol B 23-acetate from Alisma orientale (Sam.) Juz. in rat plasma using diazepam as an internal standard (IS). The plasma samples were extracted by liquid–liquid extraction with methyl tert-butyl ether and separated on a Venusil MP C18 column (100 mm × 2.1 mm, 3.0 mm) (Venusil, China) using gradient elution with the mobile phase consisting of methanol and 0.1% acetic acid in water at a flow rate of 0.4 ml/min. The two analytes were monitored with positive electrospray ionization by multiple reaction monitoring mode (MRM). The lower limit of quantitation was 5.00 ng/ml for alisol A and 5.00 ng/ml for alisol B 23-acetate. The calibration curves were linear in the range of 5.00–2500 ng/ml for alisol A and 5–2500 ng/ml for alisol B 23-acetate. The mean extraction recoveries were above 63.8% for alisol A and 68.0% for alisol B 23-acetate from biological matrixes. Both intra-day and inter-day precision and accuracy of analytes were well within acceptance criteria (15%). The validated method was successfully applied to the pharmacokinetic study of alisol A and alisol B 23-acetate in rat plasma after oral administration of alcohol extract of Alismatis Rhizoma

BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank

SummaryWe developed a new software tool, BioJava-ModFinder, for identifying protein modifications observed in 3D structures archived in the Protein Data Bank (PDB). Information on more than 400 types of protein modifications were collected and curated from annotations in PDB, RESID, and PSI-MOD. We divided these modifications into three categories: modified residues, attachment modifications, and cross-links. We have developed a systematic method to identify these modifications in 3D protein structures. We have integrated this package with the RCSB PDB web application and added protein modification annotations to the sequence diagram and structure display. By scanning all 3D structures in the PDB using BioJava-ModFinder, we identified more than 30&nbsp;000 structures with protein modifications, which can be searched, browsed, and visualized on the RCSB PDB website.Availability and implementationBioJava-ModFinder is available as open source (LGPL license) at ( https://github.com/biojava/biojava/tree/master/biojava-modfinder ). The RCSB PDB can be accessed at http://www.rcsb.org [email protected]

Metabolomics Approach To Understand Mechanisms of β‑<i>N</i>‑Oxalyl‑l‑α,β-diaminopropionic Acid (β-ODAP) Biosynthesis in Grass Pea (<i>Lathyrus sativus</i> L.)

A study was performed to identify metabolic processes associated with β-ODAP synthesis in grass pea using a metabolomics approach. GC–MS metabolomics was performed on seedlings at 2, 6, and 25 days after sowing. A total of 141 metabolites were detected among the three time points representing much of grass pea primary metabolism, including amino acids, carbohydrates, purines, and others. Principal component analysis revealed unique metabolite profiles of grass pea tissues among the three time points. Fold change, hierarchical clustering, and orthogonal projections to latent structures-discriminant analyses, and biochemical pathway ontologies were used to characterize covariance of metabolites with β-ODAP content. The data indicates that alanine and nitrogen metabolism, cysteine and sulfur metabolism, and purine, pyrimidine, and pyridine metabolism were associated with β-ODAP metabolism. Our results reveal the metabolite profiles in grass pea development and provide insights into mechanisms of β-ODAP accumulation and degradation