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CSDB/SNFG Structure Editor: an online glycan builder with 2D and 3D structure visualization
Journal of Chemical Information and Modeling. 2021. Vol. 61. No. 10. P. 4940–4948.
Bochkov A., Toukach Ph.
This article describes features, usage, and application of an CSDB/SNFG Structure Editor, a new online tool for quick and intuitive input of carbohydrate and derivative structures using Symbol Nomenclature for Glycans (SNFG). The Editor is built on a platform of the Carbohydrate Structure Database (CSDB) and relies on its online services via the dedicated web-API. The Editor allows building of oligo- and polymeric glycan structures and supports most features of natural glycans, such as underdetermined structures, alternative branches, repeating subunits, SMILES specification of atypical monomers, and others. The vocabulary of building blocks contains 600+ monomeric residues, including 327 monosaccharides. Support for SMILES allows input and visualization of chemical structures of virtually unlimited complexity. On the other hand, the interface follows the recognized GlycanBuilder style easy to novice users. The export feature includes support for CSDB Linear, GlycoCT, WURCS, SweetDB, and Glycam notations, SMILES codes, MOL/PDB atomic coordinate formats, raster and vector SNFG images, and on-the-fly visualization as 2D structural formulas and 3D molecular models. Integration of the Editor into any web-based glycoinformatics project is straightforward and simple, similarly to any other modern JavaScript application.
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Added: June 4, 2026
Novikov A., New Journal of Chemistry 2026 Vol. - No. - Article 0
Rational design of gold-based nanocarriers for neurotherapeutics requires atomic-scale understanding of drug-material interactions. Density functional theory calculations were performed to investigate levodopa (L-DOPA) adsorption on small gold clusters (Au2–Au4) with cationic, neutral, and anionic charges, with additional validation on a larger Au10 cluster using multiple low-energy isomers. Binding free energies (ΔGbind), charge transfer, and electronic descriptors ...
Added: June 3, 2026
Boldyreva M., Mohammad R., Agareva M. et al., FRONTIERS IN ANIMAL SCIENCE 2026 Vol. 7 Article 1837838
Mammals from arid ecosystems face distinct physiological challenges: water scarcity and unpredictable food availability require the integration of energy storage, maintenance of water balance, and flexible switching between nutrients. Our previous study demonstrated lower fasting blood glucose levels in the desert rodent Acomys cahirinus (African spiny mouse), which also possesses a unique regenerative ability. The aim of ...
Added: June 3, 2026
Das A., Saikia J., Maji N. et al., ChemNanoMat 2026 Vol. 12 No. 5 Article e202500733
Developing efficient photoactive materials from bio-derived resources is vital yet challenging for achieving effective water splitting performance. In this work, nano carbon dots (CDs) of zero-dimensional (0D) were synthesized from papaya peel through a simple and eco-friendly process and subsequently anchored onto the two-dimensional (2D) layered structure of graphitic carbon nitride (g-C3N4, GCN) at various ...
Added: June 2, 2026
Wary R. R., Mahato B., Sharma N. et al., The Journal of Physical Chemistry Letters 2026 Vol. 17 No. 17 P. 5099–5107
Development of heterojunction materials is an efficient approach for enhancing photocatalytic and photoelectrochemical processes. We develop a ZnO/CuO heterojunction via Cu doping into a ZnO matrix. Structural characterization confirmed that Cu was effectively incorporated into ZnO without any structural changes. The improved optical properties and reduced charge carrier recombination of the doped samples were confirmed ...
Added: June 2, 2026
Silakov D., Системный администратор 2026 № 3 С. 28–33
В статье про платформы для разработки открытого ПО в Китае мы рассказали про GitCode – молодой проект, позиционируемый как площадка для разработчиков со всего мира. Сейчас на GitCode размещаются проекты, созданные в КНР, но некоторые из них уже известны и на международной арене. Помочь открытым проектам в становлении, развитии и расширению аудитории призван фонд OpenAtom ...
Added: June 2, 2026
Ostovari Moghaddam A., Mehrabi-Kalajahi S., Hossein Vasigh S. A. et al., The Journal of Physical Chemistry Letters 2026 Vol. 17 No. 13 P. 3978–3985
Water electrolysis is a key technology for sustainable energy conversion and hydrogen generation. Recently, high-entropy oxides (HEOs) have emerged as promising materials because they allow tuning of structural, electronic, and catalytic properties in multifunctional systems. Here, we report the synthesis of a multicomponent La(FeCoCuTiNiMnMgSnZn)O3 perovskite, and its hybridization with reduced graphene oxide (rGO) to form a ...
Added: June 1, 2026
Slivnitsin P., Mylnikov L., Engineering Applications of Artificial Intelligence 2026 Vol. 179 Article 115185
The paper describes a applied artificial intelligence task of recognition-by-components method of real objects based on the recognition of a limited set of primitives or components. The recognition-by-components makes it possible to determine the components, that compose an object, and increase the number of recognizable objects without degrading the recognition quality. Training is performed on ...
Added: May 29, 2026
Kazantseva A. V., A.V. Toropova, Khusnutdinova E. K. et al., ВАВИЛОВСКИЙ ЖУРНАЛ ГЕНЕТИКИ И СЕЛЕКЦИИ, Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук» (ИЦиГ СО РАН) (Новосибирск) 2025 Vol. 30 No. 3 P. 470–481
The development of musical abilities, including absolute pitch, musical memory, rhythm sense, and musicality, at a high degree is determined by a hereditary component (up to 68 %). The studies implementing a genome-wide linkage and association approach to musical aptitude have revealed more than 100 genetic loci. This spectrum is comprised of the genes encoding ...
Added: May 29, 2026
Mokienko O., Zisman M. A., Bobrov P. et al., American Journal of Physical Medicine and Rehabilitation 2026 Vol. 105 No. 6 P. 555–563
Brain-computer interfaces (BCIs) represent a promising technology for restoring lower limb motor functions and gait after stroke. The application of BCIs in this field is supported by a limited number of studies. The objective of the review was to systematically and critically evaluate the current evidence on the use of BCIs for lower limb function ...
Added: May 28, 2026
Kazimirov D., Rybakova E., Vitalii V. Gulevskii et al., IEEE Access 2025 Vol. 13 P. 20101–20132
The Hough (discrete Radon) transform (HT/DRT) is a digital image processing tool that has become indispensable in many application areas, ranging from general image processing to neural networks and X-ray computed tomography. The utilization of the HT in applied problems demands its computational efficiency and increased accuracy. The de facto standard algorithm for the fast ...
Added: May 28, 2026
Kazimirov D., Vitalii Gulevskii, Kroshnin A. et al., Mathematics 2026 Article 1136
The Hough transform (HT) is widely used in computer vision, tomography, and neural networks. Numerous algorithms for HT computation have been proposed, making their systematic comparison essential. However, existing comparative methodologies are either non-universal and limited to certain HT formulations, or task-oriented, relying on application-specific criteria that do not fully capture algorithmic properties. This paper ...
Added: May 28, 2026
Давидович А. С., Shestakova A., Arzumanyan N. et al., Frontiers in Psychology 2026 Vol. 17 - 2026 P. 1–18
Background:
Delay discounting refers to the tendency to choose sooner, smaller rewards over larger, later rewards. Many previous studies link this tendency positively to reward sensitivity, yet the specific mechanisms behind this association remain poorly understood. Reward sensitivity may relate to delay discounting through at least three possible pathways: increased sensitivity to reward size, increased sensitivity ...
Added: May 27, 2026
Jiménez-Grávalos F., Alexander S. Novikov, Pendás Á. M., Communications in Computational Chemistry 2026 Vol. 8 No. 2 P. 203–210
Chalcogen bonds (ChBs) are often interpreted as 𝜎-hole driven electrostatic interactions between a chalcogen atom and a Lewis base, yet their covalent character remains under active discussion. Here, we present a real-space, reference-free study of prototypical X2Ch···X– complexes (X = F, Cl; Ch = O, S) using the Interacting Quantum Atoms (IQA) energy decomposition within ...
Added: May 27, 2026
Uskov F., Korobkov S., Birin K. P. et al., Journal of Photochemistry and Photobiology A: Chemistry 2026 Vol. 474 Article 116936
Oxidation of sulfides by singlet oxygen has been extensively studied, yet the structure-photoactivity relationship of these photosensitizers remains underinvestigated. In the present work the photocatalytic performance of a set of functionalized palladium(II) porphyrinates was comprehensively investigated in the photocatalytic oxidation of sulfides to reveal mutual influence of structural peculiarities onto the photosensitizing properties. The photophysical ...
Added: May 27, 2026
М.: Институт проблем управления им. В.А. Трапезникова РАН, 2024.
В сборник вошли материалы VIII Международной научной конференции «Информационные технологии и технические средства управления» (ICCT-2024). На конференции были рассмотрены вопросы, касающиеся перспектив развития научного приборостроения в телекоммуникационных и управляющих системах, биомедицинской информатики, аппаратного и программного обеспечения информационнокоммуникационных систем, надежности, диагностики и неразрушающего контроля, систем управления и автоматизации, цифровых экосистем, управления производством и логистикой, методов математического ...
Added: May 27, 2026
Agafoshin M., Gorokhov S., Dmitriev R., Geography and Natural Resources 2024 Vol. 45 No. 4 P. 436–443
This study focuses on the role of a specific unit in the spatial structure of the migration system: the
transit region. As a consequence of a sharp increase in the number of asylum seekers and refugees, there has
been a rise in the duration of their stay in temporary accommodation centers (TACs)—the main form of their
resettlement in ...
Added: February 14, 2025
Toukach P., Analytical and Bioanalytical Chemistry 2025 Vol. 417 P. 1025–1034
Carbohydrate Structure Database (CSDB) is a curated glycan data collection and a glycoinformatic platform. In this report, its database, analytical, and other components that have appeared for the recent years, are reviewed. The major improvements were achieving close-to-full coverage on glycans from microorganisms, launching modules for glycosyltransferases and saccharide conformations, online glycan builder and 3D ...
Added: October 9, 2024
Toukach P., Glycobiology 2023 Vol. 33 No. 7 P. 528–531
Carbohydrates structures in the Carbohydrate Structure Database have been referenced to glycoepitopes from the Immune Epitope Database allowing users to explore the glycan structures in the context of epitopes they contain. Starting with an epitope, one can figure out the glycans from other organisms that share the same structural fragment, and retrieve the associated taxonomical, ...
Added: October 9, 2024
R. V. Dmitriev, Gorokhov S. A., Agafoshin M. M., R-Economy 2023 Vol. 9 No. 2 P. 140–154
Relevance. The development of central place theory has been hindered by its static nature, as it fails to capture transitions between equilibrium states in central place systems. This long-standing problem remains unsolved since the theory's inception 90 years ago. This article presents a solution by examining the cases of system unification and system breakup, where ...
Added: February 16, 2024
Dmitriev R., Горохов С. А., Пространственная экономика 2022 Т. 18 № 2 С. 38–55
Статья посвящена определению условий эволюции систем центральных мест на ранних этапах в рамках подходов «новой» и классической экономической географии. Авторы приходят к выводу, что первый из них в существующем виде не операционален по отношению к эволюционным процессам, поскольку исходит из постулатов, нарушающих аксиоматику теории центральных мест, и основывается на неверных предположениях (к примеру, о справедливости ...
Added: February 16, 2024
Dmitriev R., Географический вестник 2021 № 4(59) С. 6–17
Исследование носит методический характер и имеет целью отразить пошаговую последовательность анализа популяционной и пространственной структур системы центральных мест. Для распределения поселений по уровням иерархии автор предлагает использовать опорные таблицы, отражающие вклад каждого центрального места в накопленное значение параметра К. Мы постулируем, что теория центральных мест сама по себе позволяет распределить центральные места по уровням иерархии ...
Added: February 16, 2024
Philip V.Toukach, Egorova K. S., Computational and Structural Biotechnology Journal 2022 Vol. 20 P. 5466–5476
In this paper, we present the results of a systematic statistical analysis of the fungal glycome in comparison with the prokaryotic and protistal glycomes as described in the scientific literature and presented in the Carbohydrate Structure Database (CSDB). The monomeric and dimeric compositions of glycans, their non-carbohydrate modifications, glycosidic linkages, sizes of structures, branching degree ...
Added: October 24, 2022
Philip V Toukach, Scherbinina S. I., Frank M., Glycobiology 2022 Vol. 32 No. 6 P. 460–468
Population analysis in terms of glycosidic torsion angles is frequently used to reveal preferred conformers of glycans. However, due to high structural diversity and flexibility of carbohydrates, conformational characterization of complex glycans can be a challenging task. Herein we present a conformation module of oligosaccharide fragments occurring in natural glycan structures developed on the platform ...
Added: October 24, 2022