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URS DataBase: universe of RNA structures and their motifs
The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA–protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification.
Priority areas:
IT and mathematics
Language:
English
Springer, 2025.
This book constitutes the refereed proceedings of the 19th International Conference on Parallel Computational Technologies, PCT 2025, held in Moscow, Russia, during April 8–10, 2025.
The 31 full papers included in this volume were carefully reviewed and selected from 122 submissions. These papers were organized under the following topical sections: High Performance Architectures, Tools and Technologies; ...
Added: May 18, 2026
Ronglin Z., Wei L., Jiahong C. et al., Journal of Signal Processing Systems 2026 Vol. 98 P. 1–15
To address the need for lightweight and low-latency protection in massive resource-constrained 5G Internet of Things (IoT) systems, this paper proposes Key-Controlled Modulation Hopping and Constellation Rotation (KMHCR). KMHCR is designed as a physical-layer confidentiality-enhancement mechanism that avoids bit-wise full-payload encryption in the protection pipeline. It uses a shared key derived from channel-reciprocity secret key ...
Added: May 16, 2026
Suvorov N. M., Proceedings of the Institute for System Programming of the RAS 2026 Vol. 38 No. 3(2) P. 49–66
Data Petri Nets (DPNs) extend classical Petri nets to model processes where data directly influences control-flow, enabling a comprehensive view of system behavior and possibility to detect failure points that could otherwise be hidden. Soundness is a correctness criterion that captures such failure points as deadlocks and livelocks as well as model boundedness and absence ...
Added: May 16, 2026
Mkrtchyan N. V., Regional Research of Russia 2026 Vol. 16 No. 1 P. 170–181
The aim of the study is to assess the provision of all settlements in four regions of the Near North of Russia (Vologda, Kostroma, Kirov, and Yaroslavl oblasts) with social infrastructure institutions and to analyze whether the migration balance of settlements is associated with different provision of these institutions. The study was conducted using data ...
Added: May 16, 2026
Gaeva D. V., Barinova G. M., Romanchuk A. Y., Theoretical and Applied Climatology 2026 Vol. 157 Article 302
The objective of the paper was the spatio-temporal analysis of the dynamics of extreme climate indices for the south-eastern coast of the Baltic Sea over the 40-year period 1981–2020, employing 10 extreme indices proposed by Expert Team (ET) on Climate Change Detection and Indices (ETCCDI), characterizing hazardous phenomena as: extremely high temperatures, heat waves and ...
Added: May 13, 2026
Mkrtchyan N. V., Известия РАН. Серия географическая 2026 Т. 90 № 1 С. 231–245
Objective of the study is to assess the provision of all settlements in four regions of the Russian Near
North (Vologda, Kostroma, Kirov, and Yaroslavl oblasts) with social infrastructure facilities and to
analyze whether the migration balance of settlements is associated with varying levels of provision of
these facilities. The study is based on data collected from open ...
Added: May 13, 2026
Neal N. X., Weiqing L., Dacheng H. et al., Algorithms 2026 Vol. 19 No. 5 P. 1–22
In the era of data-driven education, educational social networks generate large volumes of high-dimensional and complex-structured data through learner interactions, collaborative activities, and resource-sharing behaviors, posing significant challenges to traditional unsupervised learning methods. Such data often exhibit non-convex distributions, heterogeneity, and noise sensitivity, making conventional clustering approaches insufficient for capturing their intrinsic structural relationships. To ...
Added: May 13, 2026
Velichkov B., Nikolova-Koleva I., Slavcheva M., Shumen: INCOMA Ltd, 2025.
The RANLP 2025 Student Research Workshop (RANLPStud’2025) is a special track of the established international conference Recent Advances in Natural Language Processing (RANLP’2025).
The RANLPStud is being organised for the 9th time and this year is running in parallel with the other tracks of the main RANLP 2025 conference. The target of RANLPStud’25 is to be a ...
Added: May 12, 2026
Gerges M., Kosonogov V., OBM Neurobiology 2025 Vol. 9 No. 4 Article 310
Emotion regulation (ER) involves processes by which individuals modulate the intensity, duration, and expression of emotional responses, and its dysregulation is associated with a broad spectrum of psychological disorders. While traditionally conceptualized within psychological frameworks, ER is increasingly recognized as biologically grounded, involving intricate interactions between neurochemical, hormonal, and metabolic systems. This narrative review aims ...
Added: May 12, 2026
Stepanyants V., Долгов И. М., Хорошилов Г. С. et al., Труды Института системного программирования РАН 2026 Т. 38 № 3 С. 95–110
Highly automated and connected vehicles are gradually entering the market. Currently, solutions are being proposed that allow these technologies to be used for cooperative driving automation, which can significantly improve traffic safety. Such technologies and their software should be tested to ensure safety before being implemented in real systems. Verification and validation of vehicular control ...
Added: May 12, 2026
Tikhonov R., Efendiev M. T., Fedotenkov A. A., 2026 International Russian Smart Industry Conference (SmartIndustryCon) 2026 P. 542–547
High-fidelity simulation environments like CARLA and ROS are essential for connected and automated vehicle research. They allow researchers to verify and validate new software and technology without the time, financial, and safety overheads of real-world testing. However, their operation requires considerable expertise for creating platform-specific scenario configuration files, which complicates the research workflow. This paper ...
Added: May 11, 2026
Los Alamitos: IEEE Computer Society, 2026.
It is a great pleasure for us to welcome you on behalf of the conference committees, to the 11th IEEE International Conference on Smart Cloud (IEEE SmartCloud 2026), we are glad that we can have this international conference in New York city, USA. Now, please allow us to introduce the IEEE SmartCloud 2026 conference. The ...
Added: May 10, 2026
Avdoshin S. M., Pesotskaya E. Y., Информационные технологии 2026 Т. 32 № 4 С. 185–194
With the rapid advancement of artificial intelligence, and deep learning in particular, models have emerged that are capable of delivering highly accurate predictions. However, the internal logic of such models remains difficult to interpret—an issue of critical importance, especially in domains where the correctness of an algorithm directly affects high-stakes decision-making. One promising avenue for ...
Added: May 8, 2026
Avdoshin S. M., Pesotskaya E. Y., Business Informatics 2026 Vol. 20 No. 1 P. 7–28
The rapid development of artificial intelligence (AI) is accompanied by increasing computational
complexity and decreasing model transparency, which significantly limits its adoption in critical
domains that require a high level of trust, interpretability, and justification of decisions. Under these
conditions, the field of Explainable Artificial Intelligence (XAI) has gained particular importance as it
focuses on approaches and technologies that ...
Added: May 8, 2026
Varnavsky A., IEEE Access 2026 Vol. 14 P. 37487–37508
Puzzles are an excellent tool for learning computer science and programming, fostering increased interest, engagement, and motivation among students, as well as developing logical, critical, and computational thinking. Among beginner programmers, Parson's Programming Puzzles are quite popular, aimed at mastering the basic syntactic and logical constructs of programming languages. However, as students' skills grow, their ...
Added: May 7, 2026
Ismagilov T., Mukosey A., Smirnov F. et al., International Journal of High Performance Computing Applications 2026 Vol. 40 No. 2 P. 240–253
One of the most important aspects of supercomputer development in the post-Moore era is the interconnect technologies that allow one to unite a multitude of processing elements into a well-synchronized computing system. Novel types of supercomputer interconnect require careful benchmarking and compliance with the requirements of modern hardware trends. GPU-based heterogeneous computing is one of ...
Added: May 7, 2026
Feurra M., Perevoznyuk G., Ragimova A. et al., Scientific Reports 2026 No. 16 Article 13098 (2026)
Motor imagery (MI) allows individuals to mentally simulate movements without execution, engaging neural pathways that overlap with those used during real actions. However, how imagery perspective influences corticospinal excitability across different effectors remains unclear. Using neuronavigated transcranial magnetic stimulation (TMS), we compared kinesthetic (KMI), first-person visual (VMI-1PP), and third-person visual (VMI-3PP) imagery of elbow flexion-extension ...
Added: May 5, 2026
Yasnitsky L., Голдобин М. А., Мезенцев А. С., Прикладная математика и вопросы управления 2025 № 2 С. 99–116
Представлен обзор современных методов и основанных на них программных
инструментах, применяемых для математического моделирования серийных производственных процессов с целью снижения брака и повышения качества производимых изделий. Перечисляются группы работ, нацеленных на обнаружение и классификацию дефектов, работ, в которых решаются задачи прогнозирования образования дефектов и определения значимости параметров, работ направленных на поиск
оптимального сочетания технологических параметров изготовления изделий, ...
Added: May 5, 2026
Зайцев А. И., Pelinovsky E., Костенко И. С. et al., Морской гидрофизический журнал 2026 Т. 42 № 2 С. 263–274
Purpose. The purpose of this study is to investigate the parameters of the Kamchatka tsunami induced by the earthquake of July 29 (30), 2025, off the Kamchatka Peninsula, and its manifestations on the northern coast of Shumshu Island (Northern Kuril Islands), based on field survey results and numerical simulations. Methods and Results. The results of ...
Added: May 4, 2026
Монахова Э. А., Монахов О. Г., Rzaev E. et al., Прикладная дискретная математика 2026 Т. 71 С. 112–127
В настоящей работе исследовано совместное конструирование топологий семейств оптимальных по диаметру циркулянтных сетей $C(N; \pm 1, \pm s_2)$ и реализуемых для них оптимальных алгоритмов маршрутизации сложности $O(1)$. Предлагаемый алгоритм маршрутизации основан на использовании масштабируемых параметров $L$-образных шаблонов плотной укладки графов на плоскости для семейств оптимальных сетей.
Определены аналитические формулы зависимости этих параметров от диаметра графов семейств ...
Added: May 4, 2026
Sosnin E. I., Vasil’ev Y. L., R.A. Solovyev et al., Computer Optics 2025 Vol. 49 No. 6 P. 1129–1137
In this article, we present a new unique dataset for dental research – AlphaDent. This dataset is based on the DSLR camera photographs of the teeth of 295 patients and contains over 1200 images. The dataset is labeled for solving the instance segmentation problem and is divided into 9 classes. The article provides a detailed ...
Added: May 4, 2026
Derkacheva A., Sakirkina M., Kraev G. et al., /. 2026.
Comprehensive data on natural hazards and their consequences are crucial for effective for risk assessment, adaptation planning, and emergency response. However, many countries face challenges with fragmented, inconsistent, and inaccessible data, particularly regarding local-scale events. To address this data gap in Russia, we developed an end-to-end processing pipeline that scrapes news from various online sources, ...
Added: April 28, 2026
Qin X., Deng Y., Shchur L. et al., / Series arXiv "math". 2026. No. 2603.02962.
We perform a Monte Carlo analysis of the Ising model on many three-dimensional lattices. By means of finite-size scaling we obtain the critical points and determine the scaling dimensions. As expected, the critical exponents agree with the three-dimensional Ising universality class for all models. The irrelevant field, as revealed by the correction-to-scaling amplitudes, appears to ...
Added: April 20, 2026
Pilé I., Deng Y., Shchur L., / Series arXiv "math". 2026. No. 2604.10254.
We investigate the spatial overlap of successive spin configurations in Markov chain Monte Carlo simulations using the local Metropolis algorithm and the Svendsen-Wang and Wolff cluster algorithms. We examine the dynamics of these algorithms for two models in different universality classes: the Ising model and the Potts model with three components. The overlap of two ...
Added: April 20, 2026