Structural Database Research Articles

Phytochemical Study, Evaluation of Antihelminthic Potential and In silico Screening for Breast Cancer Using Mimosa pudica Linn.

Breast Cancer is a major health concern in India, where it is highly lethal for women because of unchecked cell proliferation and metastasis, which are frequently caused by interactions between the Estrogen Receptor Alpha and other receptors. Even though they work well, synthetic Anthelmintics come with dangers to the health of both humans and animals. Therefore, creating effective and safe Anthelmintics from plant sources is our main goal. We extracted Mimosa pudica leaves with ethanol using a Soxhlet system, and after concentration, we examined the extract using GC-MS, FTIR, and UV techniques. Estrogen Receptor structure and flavonoid compound databases from PubChem and Protein Data Bank were used for in silico testing against Breast Cancer and anthelmintic action, respectively. Using molecular docking and drug similarity investigations, the effectiveness of natural compounds against Breast Cancer was evaluated.

What Is Rural Well‐Being and How Is It Measured? An Attempt to Order Chaos*

AbstractWhile a substantial body of literature has been built on rural well‐being, due to the great heterogeneity of rural territories, the literature is highly fragmented, even contradictory. Moreover, no systematic review of the entire domain exists to guide rural decision‐makers. Debated conceptualization, contradicting results, and pressing policy requirements make it timely to deliver a systematized state‐of‐the‐art on rural well‐being to anchor public policies in the rural development domain. By systematically reviewing the scholarly literature on rural well‐being and all documents developed by government and private entities that academia highlighted as relevant to this subject, the study provides a bibliometric and thematic analysis of the domain without a time limit. Thirty‐three rural well‐being dimensions and over 9,000 indicators within these dimensions have been identified, their interconnections established and their relevance to international development goals highlighted. The study presents the structure and content of this indicator database and provides suggestions for rural researchers and policymakers on how to use it to build their own well‐being framework. It also provides an overview of each rural well‐being dimension by discussing the key theories, the main inconsistencies, the most relevant studies and authors, the fundamental measurement frameworks, and the indicators used.

Analysis of COF-300 synthesis: probing degradation processes and 3D electron diffraction structure.

Although COF-300 is often used as an example to study the synthesis and structure of (3D) covalent organic frameworks (COFs), knowledge of the underlying synthetic processes is still fragmented. Here, an optimized synthetic procedure based on a combination of linker protection and modulation was applied. Using this approach, the influence of time and temperature on the synthesis of COF-300 was studied. Synthesis times that were too short produced materials with limited crystallinity and porosity, lacking the typical pore flexibility associated with COF-300. On the other hand, synthesis times that weretoo long could be characterized by loss of crystallinity and pore order by degradation of the tetrakis(4-aminophenyl)methane (TAM) linker used. The presence of the degradation product was confirmed by visual inspection, Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). As TAM is by far the most popular linker for the synthesis of 3D COFs, this degradation process might be one of the reasons why the development of 3D COFs is still lagging compared with 2D COFs. However, COF crystals obtained via an optimized procedure could be structurally probed using 3D electron diffraction (3DED). The 3DED analysis resulted in a full structure determination of COF-300 at atomic resolution with satisfying data parameters. Comparison of our 3DED-derived structural model with previously reported single-crystal X-ray diffraction data for this material, as well as parameters derived from the Cambridge Structural Database, demonstrates the high accuracy of the 3DED method for structure determination. This validation might accelerate the exploitation of 3DED as a structure determination technique for COFs and other porous materials.

Research on Dynamic Updating Technology of Digital Maps for Mobile Communications Based on Multi source Remote Sensing Images

Abstract. With the rapid development of 5G networks in China, mobile communication network simulation technology has gradually become a widely studied direction in the academic and application fields. This study focuses on three-dimensional digital geographic information data for mobile communication, including a large amount of geographic information data that significantly affects the propagation of mobile communication radio waves, such as terrain height and ground use types. These data play a crucial role in coverage prediction, interference analysis, and frequency planning in various telecommunications planning software. This article starts from the perspective of mobile communication network management, and combines typical large-scale terrain data production practice projects for mobile communication to deeply study the process and system function design of combining geographic information systems with multi-source remote sensing data in mobile communication network monitoring and management. On this basis, this study designed and implemented a dynamic updated terrain database for mobile communication. This database can update geographic information data in real-time, ensuring the timeliness and accuracy of the data. At the same time, by optimizing the database structure and query algorithms, the speed and efficiency of data processing have been improved, providing efficient and reliable solutions for coverage prediction, optimization analysis, and planning management of large-scale mobile communication networks.In summary, dynamic updating database of three-dimensional digital geographic information has important application value in mobile communication network simulation technology. Through in-depth research and application of this database, the performance and service quality of mobile communication networks can be effectively improved, laying a solid foundation for future communication technology development.

Relativistic atomic structure calculations of Li-like ions used for plasma diagnostic studies

Abstract We have carried out atomic structure calculations using systematically enlarged multiconfiguration Dirac- Fock wavefunctions of Li-like ions of the most prominent plasma impurities (Ar, Ti, Fe, Ni, Kr and W) found in presently working tokamaks. Relativistic Breit interaction and quantum electrodynamic (QED) corrections such as vacuum polarization and self-energy corrections are also included in the calculations prior to the evaluation of low lying energy levels, transition probabilities, oscillator strengths and line strengths. Selective radiative data for electric dipole and magnetic quadrupole transitions are also reported. Special emphasis is given in the computations of fundamental quantities such as oscillator strengths as they are widely used in atomic data and analysis structure (ADAS) databases to evaluate quantities such as effective collision strengths. Present com- puted values are compared with existing available results on NIST database and few similar earlier computations and a good agreement has been found. We believe that the detailed atomic data with the relativistic and QED corrections will assist in spectroscopic studies such as accurate line identification and plasma modelling work in tokamak plasma, laser induced breakdown spectroscopy (LIBS), highly charged ions clocks and astrophysical observations.

Major structural types in inorganic chemistry and mineralogy: New data

Research subject. Structural types with different stoichiometric correlations between chemical elements. Aim. To analyze the prevalence of structural types with different stoichiometric correlations between chemical elements, such as simple substances with binary compounds, triple compounds with stoichiometry ABX3, triple compounds with stoichiometry AB2X4. Key points. The analysis was conducted using the databases of inorganic compounds ICSD (Inorganic Crystal Structure Database) and PCD (Pearson’s Crystal Data). The number of entries with the most typical structural types for 2013 and 2023 are determined. Their classifications in various databases for different years are given. The ranks of structural types for minerals and inorganic compounds are analyzed. The minerals crystallized in all the considered structural types are indicated according to the 2023 ISCD data, sampling only by the number of minerals registered in IMA (International Mineralogical Association – Commission on New Minerals, Nomenclature and Classification) for March 2023. The Russian names of minerals are presented in accordance with the database WWW-MINCRIST for the minerals crystallizing in all the structural types under consideration. Conclusions. The most probable causes for the realization of each stoichiometric correlation in various structural types are determined. The prevalence of certain structural types among inorganic compounds and minerals, as well as the underlying reasons, are discussed based on the principles of crystal chemistry.

Accelerating material property prediction using generically complete isometry invariants

Periodic material or crystal property prediction using machine learning has grown popular in recent years as it provides a computationally efficient replacement for classical simulation methods. A crucial first step for any of these algorithms is the representation used for a periodic crystal. While similar objects like molecules and proteins have a finite number of atoms and their representation can be built based upon a finite point cloud interpretation, periodic crystals are unbounded in size, making their representation more challenging. In the present work, we adapt the Pointwise Distance Distribution (PDD), a continuous and generically complete isometry invariant for periodic point sets, as a representation for our learning algorithm. The PDD distinguished all (more than 660 thousand) periodic crystals in the Cambridge Structural Database as purely periodic sets of points without atomic types. We develop a transformer model with a modified self-attention mechanism that combines PDD with compositional information via a spatial encoding method. This model is tested on the crystals of the Materials Project and Jarvis-DFT databases and shown to produce accuracy on par with state-of-the-art methods while being several times faster in both training and prediction time.

The geographic and phylogenetic structure of public DNA barcode databases: an assessment using Chrysomelidae (leaf beetles)

IntroductionDNA barcoding in insects has progressed rapidly, with the ultimate goal of a complete inventory of the world’s species. However, the barcoding effort to date has been driven by a few national campaigns and leaves much of the world unsampled. This study investigates to what degree the current barcode data cover the species diversity across the globe, using the leaf beetle family Chrysomelidae as an example.MethodsA recent version (June 2023) of the Barcode-of-Life database was subjected to test of sampling completeness using the barcode-to-BIN ratio and sampling coverage (SC) metric. All barcodes were placed in a phylogenetic tree of ~600 mitochondrial genomes, applying phylogenetic diversity (PD) and metrics of community phylogenetics to national barcode sets to test for sampling completeness at clade level and reveal the global structure of species diversity.ResultsThe database included 73342 barcodes, grouped into 5310 BINs (species proxies) from 101 countries. Costa Rica contributed nearly half of all barcode sequences, while nearly 50 countries were represented by less than ten barcodes. Only five countries, Costa Rica, Canada, South Africa, Germany, and Spain, had a high sampling completeness, although collectively the barcode database covers most major taxonomic and biogeographically confined lineages. PD showed moderate saturation as more species diversity is added in a country, and community phylogenetics indicated clustering of national faunas. However, at the species level the inventory remained incomplete even in the most intensely sampled countries, and the sampling was insufficient for assessment of global species richness patterns.DiscussionThe sequence-based inventory in Chrysomelidae needs to be greatly expanded to include more areas and deeper local sampling before reaching a knowledge base similar to the existing Linnaean taxonomy. However, placing the barcodes into a backbone phylogenetic tree from mitochondrial genomes, a taxonomically and biogeographically highly structured pattern of global diversity emerges into which all species can be integrated via their barcodes.

Copyright for Computer Programs and Databases

In the digital age, computer programs and databases have emerged as invaluable intellectual properties, driving technological advancements and innovation across industries. As these works become increasingly critical to modern society, ensuring adequate legal protection through copyright law is paramount. This article explores the intricate legal landscape surrounding copyright protection for computer programs and databases. Focusing on the international and national legal frameworks, the article examines the requirements for copyright eligibility, such as originality, fixation, and authorship. It delves into the scope of protection, encompassing source code, object code, user interfaces for computer programs, and the structure, arrangement, and data content of databases. The article also addresses the exceptions and limitations to copyright protection, balancing the rights of creators with the legitimate interests of users and the public. Fair use, reverse engineering, and the creation of backup copies are among the key exceptions discussed. Additionally, the article highlights the challenges of enforcing copyright protection in the digital realm, including digital piracy, transnational infringement, and the complexities surrounding technological protection measures. By providing a comprehensive overview of this intricate legal domain, the article aims to foster a deeper understanding of the critical role copyright plays in incentivizing innovation and creativity in the digital age, while also acknowledging the need for a balanced approach that promotes access and legitimate use of these invaluable works

Visual Cryptography Based Authentication with AES for the Data

Abstract: In the rapidly evolving digital era, ensuring the security and integrity of data has become a critical priority, particularly with the widespread proliferation of sensitive information across diverse digital platforms. While traditional encryption techniques have demonstrated efficacy, they often encounter challenges such as data format alterations and potential disruptions to existing systems. To surmount these hurdles, this paper proposes an innovative encryption paradigm that amalgamates Advanced Encryption Standard (AES), eXclusive OR (XOR) operation, and a tailored translation methodology meticulously crafted to uphold data format fidelity. This novel approach not only streamlines database modifications but also fortifies security measures. Through a rigorous comparative analysis with extant encryption methodologies, the efficacy and security advantages of the proposed framework are underscored. By seamlessly integrating cryptographic principles and AES, the envisioned solution ensures data confidentiality while preserving database performance and structure integrity, thus furnishing a robust framework for safeguarding sensitive information in today's dynamic digital milieu.

Perancangan Sistem Informasi Peminjaman dan Pengembalian Berkas Rekam Medis Rawat Jalan dengan Metode Waterfall

Wiyung Sejahtera Hospital in recording the borrowing and returning of outpatient medical records still uses expedition books which are recorded manually. The research aims to design and develop an information system to facilitate the process of borrowing and returning outpatient medical record files using the Waterfall method approach. The Waterfall method was chosen because of its ability to divide system development into structured stages, starting from requirements analysis to maintenance. The needs analysis stage involves an in-depth study of existing processes and user needs. Next, system design is carried out by building a design plan that includes database structure, user interface design, and system workflow. System implementation is carried out by developing applications based on previous designs, while system testing is carried out thoroughly to ensure quality and performance before full implementation. The maintenance stage is carried out to ensure system operation and carry out continuous repairs and improvements. As a result, it is hoped that this system can improve the efficiency and quality of outpatient medical record file management and health services as a whole. The conclusion of this research is the successful design and development of a computer-based information system for borrowing and returning outpatient medical records at Wiyung Sejahtera Hospital using the waterfall method.

Enhancing Security in Industrial Application Development: Case Study on Self-Generating Artificial Intelligence Tools

The emergence of security vulnerabilities and risks in software development assisted by self-generated tools, particularly with regard to the generation of code that lacks due consideration of security measures, could have significant consequences for industry and its organizations. This manuscript aims to demonstrate how such self-generative vulnerabilities manifest in software programming, through a case study. To this end, this work undertakes a methodology that illustrates a practical example of vulnerability existing in the code generated using an AI model such as ChatGPT, showcasing the creation of a web application database, SQL queries, and PHP server-side. At the same time, the experimentation details a step-by-step SQL injection attack process, highlighting the hacker’s actions to exploit the vulnerability in the website’s database structure, through iterative testing and executing SQL commands to gain access to sensitive data. Recommendations on effective prevention strategies include training programs, error analysis, responsible attitude, integration of tools and audits in software development, and collaboration with third parties. As a result, this manuscript discusses compliance with regulatory frameworks such as GDPR and HIPAA, along with the adoption of standards such as ISO/IEC 27002 or ISA/IEC 62443, for industrial applications. Such measures lead to the conclusion that incorporating secure coding standards and guideline—from organizations such as OWASP and CERT training programs—further strengthens defenses against vulnerabilities introduced by AI-generated code and novice programming errors, ultimately improving overall security and regulatory compliance.

In silico structures, mass spectra and retention indices database development for purposes of chemical weapons convention

The Chemical Weapons Convention (CWC) is a science-based international treaty for the disarmament and non-proliferation of chemical weapons. However, reference Orgaization for prohibition of chemical weapons (OPCW) central analytical database (OCAD) of structures with mass spectra (MS) and retention indices (RI) includes only minor part of all possible chemical species defined in the Schedules of CWC. In this work we employed OCAD in silico augmentation based on chemoinformatics approach for chemical structures enumeration, MS data generation based on message passing neural network and based on P-alkyl molecular pairs RI prediction to support the verification activities as provided for in the CWC. Enumerated 879 noncyclic and 5270 monocyclic alcohols became the basis for generating hundreds of thousands molecules of Schedule 1 toxic chemicals like Sarin, Tabun, VX and Novichok. Trained on ordinary and neutral loss electron ionization mass spectrometry (EI-MS) a message-passing neural network (MPNN) outperformed other quantum chemistry and machine learning methods. Generated by this MPNN in silico EI-MS are very similar to the library's spectra and allowed to reach desired match factor above 800 within a scale of 0–1000. Statistical data for molecular pairs based on P-alkyl fragments was collected and used to predict RIs within desired 20 RI window for some toxic chemicals of Schedule 1.A.01, for which in the current OCAD version RIs are absent.

In – Silico Biological Evaluation of Antifungal Drugs - Molinspiration

The aim of this research work is to evaluate In – Silico Antifungal Drugs, in this work Molinspiration is used to provide predictive tools for essential molecular properties, such as lipophilicity, aqueous solubility and pKa, which are critical in drug discovery and cheminformatics. It operates based on a comprehensive database of chemical structures and employs algorithms to calculate these properties. Molinspiration is a renowned software and informatics company that plays a pivotal role in the pharmaceutical and biotechnology industries. With a primary focus on providing cutting-edge cheminformatics tools and software solutions, Molinspiration has significantly contributed to the field of drug discovery and medicinal chemistry.  Molinspiration's software is an indispensable resource for the pharmaceutical and biotechnology sectors.

DMXP: A De Novo Small-Molecule 3D Structure Predictor with Graph Attention Networks.

Generating the three-dimensional (3D) structure of small molecules is crucial in both structure- and ligand-based drug design. Structure-based drug design needs bioactive conformations of compounds for lead identification and optimization. Ligand-based drug design techniques, such as 3D shape similarity search, 3D pharmacophore model, 3D-QSAR, etc., all require high-quality small-molecule ligand conformations to obtain reliable results. Although predicting a small molecular bioactive conformer requires information from the receptor, a crystal structure of the molecule is a proper approximation to its bioactive conformer in a specific receptor because the binding pose of a small molecule in its receptor's binding pockets should be energetically close to the crystal structures. This study presents a de novo small molecular structure predictor (dMXP) with graph attention networks based on crystal data derived from the Cambridge Structural Database (CSD) combined with molecular electrostatic information calculated by density-functional theory (DFT). Two featuring strategies (topological and atomic partial change features) were employed to explore the relation between these features and the 3D crystal structure of a small molecule. These features were then assembled to construct the holistic 3D crystal structure of a molecule. Molecular graphs were encoded using a graph attention mechanism to deal with the issues of the inconsistencies of local substructures contributing to the entire molecular structure. The root-mean-square deviation (RMSDs) of approximately 80% dMXP predicted structures and the native binding poses within receptors are less than 2.0 Å.

Educational Web Portal Software for Teachers, Tutors and Students

This article substantiates the feasibility of using the Data-Driven approach in education and creating a "one-stop shop" platform. The paper describes the advantages and disadvantages of modern domestic and foreign ED Tech products, on the basis of which a conclusion is made about the necessary functionality of the designed platform. The article describes the software requirements for the UML design methodology, describes the choice of creation tools, and considers the program for implementing the tool system, including the database structure. It is shown that such a scheme is scalable and can be easily supplemented with other functionality. Based on the requirements, a project prototype was created, located at kuzovkin.info; the project consists of several parts, including a database with tasks, an online simulator, an online board, a voice messenger and articles with task theory. In addition, in the future, it is planned to use an adaptive learning algorithm using artificial intelligence. It is shown that this prototype is successfully used for teaching students. In the future, a web portal with similar tools is planned to be introduced into the work of online schools.

Can AlphaFold's breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity?

T cells are essential immune cells responsible for identifying and eliminating pathogens. Through interactions between their T-cell antigen receptors (TCRs) and antigens presented by major histocompatibility complex molecules (MHCs) or MHC-like molecules, T cells discriminate foreign and self peptides. Determining the fundamental principles that govern these interactions has important implications in numerous medical contexts. However, reconstructing a map between T cells and their antagonist antigens remains an open challenge for the field of immunology, and success of in silico reconstructions of this relationship has remained incremental. In this Perspective, we discuss the role that new state-of-the-art deep-learning models for predicting protein structure may play in resolving some of the unanswered questions the field faces linking TCR and peptide-MHC properties to T-cell specificity. We provide a comprehensive overview of structural databases and the evolution of predictive models, and highlight the breakthrough AlphaFold provided the field.

Halogen Bond via an Electrophilic π-Hole on Halogen in Molecules: Does It Exist?

This study reveals a new non-covalent interaction called a π-hole halogen bond, which is directional and potentially non-linear compared to its sister analog (σ-hole halogen bond). A π-hole is shown here to be observed on the surface of halogen in halogenated molecules, which can be tempered to display the aptness to form a π-hole halogen bond with a series of electron density-rich sites (Lewis bases) hosted individually by 32 other partner molecules. The [MP2/aug-cc-pVTZ] level characteristics of the π-hole halogen bonds in 33 binary complexes obtained from the charge density approaches (quantum theory of intramolecular atoms, molecular electrostatic surface potential, independent gradient model (IGM-δginter)), intermolecular geometries and energies, and second-order hyperconjugative charge transfer analyses are discussed, which are similar to other non-covalent interactions. That a π-hole can be observed on halogen in halogenated molecules is substantiated by experimentally reported crystals documented in the Cambridge Crystal Structure Database. The importance of the π-hole halogen bond in the design and growth of chemical systems in synthetic chemistry, crystallography, and crystal engineering is yet to be fully explicated.

Symmetry classification of 2D materials: layer groups versus space groups

The symmetry of a crystal structure with a three-dimensional (3D) lattice can be classified by one of the 230 space group types. For some types of crystals, e.g. crystalline films, surfaces, or planar interfaces, it is more appropriate to assume a two-dimensional (2D) lattice. With this assumption the structure can be classified by one of the 80 layer group types. We have implemented an algorithm to determine the layer group type of a 3D structure with a 2D lattice, and applied it to more than 15 000 monolayer structures in the Computational 2D Materials Database (C2DB). We compare the classification of monolayers by layer groups and space groups, respectively. The latter is defined as the space group of the 3D bulk structure obtained by repeating the monolayer periodically in the direction perpendicular to the 2D lattice (AA-stacking). By this correspondence, nine pairs of layer group types are mapped to the same space group type due to the inability of the space group to distinguish the in-plane and out-of-plane axes. In total 18% of the monolayers in the C2DB belong to one of these layer group pairs and are thus not properly classified by the space group type. Our results show that symmetry classification of 2D materials should be based on layer groups rather than the commonly used space groups.

Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development.

Metal-based complexes with their unique chemical properties, including multiple oxidation states, radio-nuclear capabilities and various coordination geometries yield value as potential pharmaceuticals. Understanding the interactions between metals and biological systems will prove key for site-specific coordination of new metal-based lead compounds. This study merges the concepts of target coordination with fragment-based drug methodologies, supported by varying the anomalous scattering of rhenium along with infrared spectroscopy, and has identified rhenium metal sites bound covalently with two amino acid types within the model protein. A time-based series of lysozyme-rhenium-imidazole (HEWL-Re-Imi) crystals was analysed systematically over a span of 38 weeks. The main rhenium covalent coordination is observed at His15, Asp101 and Asp119. Weak (i.e. noncovalent) interactions are observed at other aspartic, asparagine, proline, tyrosine and tryptophan side chains. Detailed bond distance comparisons, including precision estimates, are reported, utilizing the diffraction precision index supplemented with small-molecule data from the Cambridge Structural Database. Key findings include changes in the protein structure induced at the rhenium metal binding site, not observed in similar metal-free structures. The binding sites are typically found along the solvent-channel-accessible protein surface. The three primary covalent metal binding sites are consistent throughout the time series, whereas binding to neighbouring amino acid residues changes through the time series. Co-crystallization was used, consistently yielding crystals four days after setup. After crystal formation, soaking of the compound into the crystal over 38 weeks is continued and explains these structural adjustments. It is the covalent bond stability at the three sites, their proximity to the solvent channel and the movement of residues to accommodate the metal that are important, and may prove useful for future radiopharmaceutical development including target modification.