?
Производительность современных вычислительных платформ в расчетах молекулярной динамики белок - мембранных систем
Труды НИИСИ РАН. 2018. Т. 7. № 4. С. 157-161.
The performance of molecular dynamics software package Gromacs was measured on various
hardware: desktop computers, clusters based on x84_64 processors or many integrated core processors, and
heterogeneous system with gaming graphic cards or general purpose GPU systems. The optimal choice of hardware
for molecular dynamics simulations is discussed.
Priority areas:
IT and mathematics
Language:
Russian
Krylov N., Nolde D., Телегин П. Н. et al., Труды НИИСИ РАН 2018 Т. 8 № 6 С. 74-78
We studied the performance of two algorithms for processing results of molecular dynamics (MD)
simulation on modern computing platforms: calculations of radial distribution function (RDF) and energies. We found
that both algorithms effectively parallelize both on systems with shared memory and on clusters with distributed
memory. For processing the results of medium-sized MD systems, the parallelization efficiency of ...
Added: February 10, 2020
Chugunov A.O., Volynsky P. E., Krylov N.A. et al., Scientific Reports 2016 Vol. 6 P. 33112
Heat-activated transient receptor potential channel TRPV1 is one of the most studied eukaryotic proteins involved in temperature sensation. Upon heating, it exhibits rapid reversible pore gating, which depolarizes neurons and generates action potentials. Underlying molecular details of such effects in the pore region of TRPV1 is of a crucial importance to control temperature responses of ...
Added: February 10, 2020
Volynsky P. E., Nolde D.E., Zakharova G. S. et al., Scientific Reports 2019 Vol. 9 P. 413
How is a water-soluble globular protein able to spontaneously cross a cellular membrane? It is commonly accepted that it undergoes significant structural rearrangements on the lipid-water interface, thus acquiring membrane binding and penetration ability. In this study molecular dynamics (MD) simulations have been used to explore large-scale conformational changes of the globular viscumin A chain ...
Added: February 10, 2020
Panina I., Krylov N., Nolde D. et al., Scientific Reports 2020 Vol. 10 Article 8821
Antibiotics (AB) resistance is a major threat to global health, thus the development of novel AB classes is urgently needed. Lantibiotics (i.e. nisin) are natural compounds that effectively control bacterial populations, yet their clinical potential is very limited. Nisin targets membrane-embedded cell wall precursor — lipid II — via capturing its pyrophosphate group (PPi), which is unlikely ...
Added: June 1, 2020
Krylov N., Efremov R., BMC Research Notes 2021 Vol. 14 Article 124
Objective: The purpose of this work is to optimize the processing of molecular dynamics (MD) trajectory data
obtained for large biomolecular systems. Two popular software tools were chosen as the reference: the tng and
the xdrfile libraries. Current implementation of tng algorithms and library is either fast or storage efficient and
xdrfile is storage efficient but slow. Our ...
Added: August 24, 2021
Panina I., Chugunov A., Nolde D. et al., FEBS Open Bio 2021 Vol. 11 No. Suppl.1 P. 356-356
Given the challenge of global antibiotic resistance, the development of new medications is indispensable. Lipid II - bacterial cell wall precursor – is a promising pharmaceutical target for innovative antibiotics, whereas lantibiotic nisin, effectively capturing lipid II’s conservative pyrophosphate group, is a potential prototype of a new generation of antibiotics. Because the structure of membrane-bound ...
Added: August 31, 2021
Fomin D., Математические вопросы криптографии 2015 Vol. 6 No. 2 P. 99-108
In this article we consider NVIDIA GPU implementation aspects of an XSL block cipher over the finite field with MDS-matrix linear transformation. We compare obtained results with some other block ciphers. ...
Added: May 4, 2019
Nadezhdin K., Neuberger A., Trofimov Y. et al., Nature Structural and Molecular Biology 2021 Vol. 28 P. 564-572
Numerous physiological functions rely on distinguishing temperature through temperature-sensitive transient receptor potential channels (thermo-TRPs). Although the function of thermo-TRPs has been studied extensively, structural determination of their heat- and cold-activated states has remained a challenge. Here, we present cryo-EM structures of the nanodisc-reconstituted wild-type mouse TRPV3 in three distinct conformations: closed, heat-activated sensitized and open ...
Added: August 24, 2021
Стройлов В. С., Панова М. А., Toukach P., International Journal of Molecular Sciences 2020 Vol. 21 No. 20 Article 7626
Six empirical force fields were tested for applicability to calculations for automated carbohydrate database filling. They were probed on eleven disaccharide molecules containing representative structural features from widespread classes of carbohydrates. The accuracy of each method was queried by predictions of nuclear Overhauser effects (NOEs) from conformational ensembles obtained from 50 to 100 ns molecular ...
Added: January 31, 2022
Panina I. S., Chugunov A., Efremov R., Russian Journal of Bioorganic Chemistry 2018 Vol. 44 No. 6 P. 653-664
The growing problem of antibiotic resistance in medicine raises the attention to antimicrobial substances that act on non-protein molecules, which have more conservative structure comparing to proteins or peptides. One of the most promising and studied targets is lipid II — the participant of the bacterial cell wall biosynthetic pathway. Lipid II is present in ...
Added: February 25, 2019
Коншина А. Г., Дубовский П. В., Efremov R., Journal of Chemical Information and Modeling 2021 Vol. 61 No. 1 P. 385-399
For many peripheral membrane-binding proteins (MBPs), especially β-structural ones, the precise molecular mechanisms of membrane insertion remain unclear. In most cases, only the terminal water-soluble and membrane-bound states have been elucidated, whereas potential functionally important intermediate stages are still not understood in sufficient detail. In this study we present one of the first successful attempts ...
Added: January 24, 2021
NY : Nova Science Publishers, Inc., 2017
In this book, the original papers have been collected that demonstrate the efficient use of the computer molecular dynamics (MD) simulation methods for the studying of nanoscale phenomena in the materials and life sciences. This volume contains the Proceedings of the International Symposium KSCMBS-2016 ”Khujand Symposium on Computational Materials and Biological Sciences” (10 th Japan–Russia ...
Added: November 14, 2017
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
Ижевск : Ижевский институт компьютерных исследований, 2017
Процессы трансформации энергии и регуляции этих процессов при изменении характеристик внешней и внутренней среды лежат в основе устойчивого существования всех живых систем. Монография содержит главы, посвященные физико-химическим механизмам регуляции процессов на молекулярном, субклеточном и клеточном уровнях. В книге описаны результаты последних достижений отечественной науки в области фолдинга белка (Финкельштейн и др.), молекулярных основ взаимодействия белков ...
Added: November 14, 2017
Goncharov R., Сапанов П. М., Яшунский А. Д., Социология власти 2013 № 3 С. 57-72
В статье представлена технология, позволяющая собирать в полевых исследованиях пространственно локализованные данные об объектах городской среды. Технология основана на автоматической привязке фотографий к пространственным координатам. Приведен план полевых и камеральных мероприятий, предложены варианты ГИС-обработки собираемых таким образом данных. В качестве примера приведены данные об использовании белорусского языка в общественном пространстве городов Белоруссии. ...
Added: April 12, 2015
Bukharov O., Mizikin A. A., Bogolyubov D., Промышленные АСУ и контроллеры 2013 № 7 С. 37-45
In this article we ground some advantages of the evolutionary approach to the solution of problems of decision support system development. The most popular methods of forecasting and detection of dependences are considered. Advantages of use of neural networks to forecast and to determine of dependences between parameters of systems are given. Advantages of interval ...
Added: November 29, 2013
Красноярск : ИВМ СО РАН, 2013
Труды Пятой Международной конференции «Системный анализ и информационные технологии» САИТ-2013 (19–25 сентября 2013 г., г.Красноярск, Россия): ...
Added: November 18, 2013
Rusinov I. S., Ershova A. S., Karyagina A. S. et al., BMC Genomics 2018 Vol. 19 No. 885 P. 1-11
Background. Restriction-modification (R-M) systems protect bacteria and archaea from attacks by bacteriophages and archaeal viruses. An R-M system specifically recognizes short sites in foreign DNA and cleaves it, while such sites in the host DNA are protected by methylation. Prokaryotic viruses have developed a number of strategies to overcome this host defense. The simplest anti-restriction ...
Added: December 20, 2018
Sorokin K., Ayzenberg A., Анохин К. В. et al., / Cornell University. Series Computer Science "arxiv.org". 2022.
In present paper we test different approaches to reconstructing the topology of the physical space from neural activity data in A1 fields of mice brains, in particular, having a Cognitome-focused approach in mind. Animals were placed in different new environments and discovered them while their physical and neural activity was recorded. We discuss possible approaches ...
Added: November 17, 2022
Voronova L.I., Trunov A. S., Voronov V.I., International journal of experimental education 2013 No. 12 P. 82-91
The model of distributed calculators makes it possible a parallel calculation of the correlated N-particle system with a complex multi-particle interaction (long-range ionic and short-range repulsive, two- and three-particle covalent interactions) with MPI and CUDA technologies. The computational model is based on the mathematical model of heterogeneous descriptors developed by the authors, that allows shift ...
Added: November 15, 2013
Baulin E., Roytberg M. A., Астахова Т. В., Математическая биология и биоинформатика 2012 Т. 7 № 2 С. 567-571
Предложена классификация элементов вторичной структуры РНК, которая является обобщением классификации петель, предложенной Мэтьюзом и Тернером. Эта классификация позволяет единообразно описывать структуры как содержащие, так и не содержащие псевдоузлы. ...
Added: January 30, 2013
Panina I., Balandin S., Tsarev A. et al., International Journal of Molecular Sciences 2023 Vol. 24 No. 2 P. 1
To date, a number of lantibiotics have been shown to use lipid II — a highly conserved peptidoglycan precursor in the cytoplasmic membrane of bacteria — as their molecular target. The α-component (Lchα) of the two-component lantibiotic lichenicidin (Lchα), previously isolated from the Bacillus licheniformis VK21 strain, seems to contain two putative lipid II binding ...
Added: February 21, 2023
[б.и.], 2019
. ...
Added: January 15, 2020
Nersisyan S., Galatenko A. V., Galatenko V. V. et al., Plos One 2021 Vol. 16 No. 4 Article e0249424
Analysis of regulatory networks is a powerful framework for identification and quantification of intracellular interactions. We introduce miRGTF-net, a novel tool for construction of miRNA-gene-TF networks. We consider multiple transcriptional and post-transcriptional interaction types, including regulation of gene and miRNA expression by transcription factors, gene silencing by miRNAs, and co-expression of host genes with their ...
Added: May 10, 2021