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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
Borovikova I., Okhrimenko G., Zamyatin V. et al., Journal of Structural Biology 2026 Vol. 218 No. 2 Article 108315
Single amino acid substitutions in the ATP-binding domain of ACVRL1, a key receptor in the bone morphogenetic protein (BMP) signaling pathway, are frequently classified as variants of uncertain significance (VUS), complicating molecular diagnosis for pulmonary arterial hypertension (PAH) and Hereditary Hemorrhagic Telangiectasia (HHT). Since aberrant ATP binding disrupts downstream SMAD1/5/8 phosphorylation, we employed molecular dynamics ...
Added: May 20, 2026
Shipilov F., Barnyakov A., Ivanov A. et al., / Series Physics "arxiv.org". 2026.
A fast simulation of the detector response is a vital task in high-energy physics (HEP). Traditional Monte-Carlo methods form the backbone of modern particle physics simulation software but are computationally expensive. We present a machine-learning-based approach to fast simulation of the Focusing Aerogel Ring Imaging Cherenkov (FARICH) detector response. Given a particle track and momentum, ...
Added: May 19, 2026
Goltseva Y., Tsokolaeva Z., Beloglazova I. et al., Stem Cell Research and Therapy 2026 Vol. 17 No. 1
Background Cardiac fibrosis represents a significant health burden, with endothelial dysfunction and damaged
perivascular microenvironment increasingly recognized as key contributors to fibrotic remodeling. The urokinase
plasminogen activator receptor (uPAR), a critical component of the urokinase system, plays a pivotal role in vascular
remodeling and fibrosis. While prior evidence indicates that uPAR deficiency leads to microvascular dysfunction and
perivascular fibrosis, ...
Added: May 19, 2026
Association for Computational Linguistics, 2026.
Added: May 19, 2026
Bezzubov S., Malikov D., Krasnov L. et al., Scientific data 2026 Vol. 13 Article 727
Solubility is a crucial property of organic compounds, impacting their potential applications in synthetic chemistry, materials science and drug design. Moreover, in technological processes mixtures of solvents are often utilized, making the solubility assessment more complicated. Predicting solubility values in mixtures of solvents from a molecular structure can help to address this issue, although a ...
Added: May 19, 2026
Pikalov V., Meshcheryakov V., Kondratev S. et al., Technologies 2026 Vol. 14 No. 1 P. 1–27
This paper presents Aerokinesis, an IoT-based software–hardware system for intuitive gesture-driven control of quadcopter unmanned aerial vehicles (UAVs), developed within the Robot Operating System 2 (ROS2) framework. The proposed system addresses the challenge of providing an accessible human–drone interaction interface for operators in scenarios where traditional remote controllers are impractical or unavailable. The architecture comprises ...
Added: May 19, 2026
Кондратьев С., Никитин Г. Э., Дырченкова Ю. А. et al., Technologies 2026 Vol. 14 No. 1 P. 1–27
This paper presents Aerokinesis, an IoT-based software–hardware system for intuitive gesture-driven control of quadcopter unmanned aerial vehicles (UAVs), developed within the Robot Operating System 2 (ROS2) framework. The proposed system addresses the challenge of providing an accessible human–drone interaction interface for operators in scenarios where traditional remote controllers are impractical or unavailable. The architecture comprises ...
Added: May 19, 2026
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
N. V. Mkrtchyan, 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
Xiong N., Long W., He D. et al., Algorithms 2026 Vol. 19 No. 5 Article 386
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
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
Gabdullin N., Androsov I., / Series Computer Science "arxiv.org". 2026.
Label prediction in neural networks (NNs) has O(n) complexity proportional to the number of classes. This holds true for classification using fully connected layers and cosine similarity with some set of class prototypes. In this paper we show that if NN latent space (LS) geometry is known and possesses specific properties, label prediction complexity can ...
Added: April 2, 2026