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691 results for “Molecular dynamics”
Dataset for: Molecular Dynamics study of the Recognition of the Nucleic Acid Aptamer to ATP
<p>Files with the initial aptamer structures (wt and three mutant forms) and their complexes with ATP after docking, used in the MD simulations, along with MD simulation trajectories and meta-eABF simulations, are included as tarballs (.tar.gz). </p> <p>Mutant structures were generated using PyMol, ATP docking performed using AutoDock Vina, and MD simulations based on NAMD software and Charmm36 and CGenFF force fields. </p> <p> </p>
All Atom Molecular Dynamics Simulations of Ritonavir at the Binding Pocket of SARS-CoV2 Main Protease
<p>Data includes all of the trajectories (2000) of classical all-atom molecular dynamics (MD) simulations of ritonavir at the binding pocket of SARS-CoV2 main protease target. In order to decrease the size of the file only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Protein–ligand complexes were obtained by Glide/SP docking program. Complex was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cutoff<br> radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310K initially, and Nose–Hoover thermostat was used for adjustment. Martyna–Tobias–Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 500 ns production run was performed for the simulation.</p> <p> </p>
All Atom Molecular Dynamics Simulations of inhibitor N3 at the binding pocket of SARS-CoV2 Main Protease (PDB ID: 6LU7)
<p>Data includes all of the trajectories (1000) of classical all-atom molecular dynamics (MD) simulations of inhibitor N3 at the binding pocket of SARS-CoV2 main protease target (PDB ID: 6LU7). In order to decrease the size of the file only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Protein–ligand complexes were obtained from RCSB PDB (PDB ID: 6LU7). Complex was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cutoff<br> radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310K initially, and Nose–Hoover thermostat was used for adjustment. Martyna–Tobias–Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 100 ns production run was performed for the simulations.</p>
Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH) (with unbound ligand)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer with unbound ligands. Simulation starts from the crystal pose (PDB: 5FII) and is motivated by this paper:</p> <p>Yunhui Ge, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
Complementary data to "Molecular dynamics trajectories for 630 drug-membrane potentials of mean force"
<p>Missing data from "Molecular dynamics trajectories for 630 drug-membrane potentials of mean force"</p> <p>Hoffmann, Christian; Centi, Alessia; Menichetti, Roberto; Bereau, Tristan (2020): Molecular dynamics trajectories for 630 drug-membrane potentials of mean force. figshare. Collection.</p> <p>https://doi.org/10.6084/m9.figshare.c.4641551.v1</p> <p>Includes:</p> <ul> <li>'bsResult.xvg' of DIM_P2-P3 in DLPC</li> </ul>
Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein (Topology and .xtc files)
<p>ABSTRACT. The recent outbreak of the respiratory syndrome-related coronavirus (SARS-CoV-2) is stimulating an unprecedented scientific campaign to alleviate the burden of the coronavirus disease (COVID-19). One line of research has focused on targeting SARS-CoV-2 proteins fundamental for its replication by repurposing drugs approved for other diseases. The first interaction between the virus and the host cell is mediated by the spike protein on the virus surface and the human angiotensin-converting enzyme (ACE2). Small molecules able to bind the receptor-binding domain (RBD) of the spike protein and disrupt the binding to ACE2 would offer an important tool for slowing, or even preventing, the infection. Here, we screened 2421 approved small molecules<em> in </em>silico and validated the docking outcomes through extensive molecular dynamics simulations. Out of six drugs characterized as putative RBD binders, the cephalosporin antibiotic cefsulodin was further assessed for its effect on the binding between the RBD and ACE2, suggesting the importance of considering the dynamic formation of the heterodimer when judging any potential candidate.</p>
Molecular dynamics simulation data of designed cyclic peptide (ligand-binding)
<p>Trajectories of ligand binding simulation and simulation set-up files of designed cyclic peptide as MDM2 binders. <br> The original paper of these designed cyclic peptide: Danelius, E., Pettersson, M., Bred, M., Min, J., Waddell, M. B., Guy, R. K., et al. (2016). Flexibility is important for inhibition of the MDM2/p53 protein–protein interaction by cyclic β-hairpins. <em>Org. Biomol. Chem.</em>, <em>14</em>(44), 10386–10393. http://doi.org/10.1039/C6OB01510G</p>
Input files and scripts for Hamiltonian replica-exchange molecular dynamics simulations of intrinsically disordered proteins using a software GROMACS patched with PLUMED
<p>Here we share the necessary files and scripts to run Hamiltonian replica-exchange molecular dynamics simulations of intrinsically disordered protein studied in the preprint uploaded to bioRxiv (doi: https://doi.org/10.1101/2020.06.16.155374). It requires software GROMACS patched with PLUMED.</p>
Predicting Hydrophobicity by Learning Spatiotemporal Features of Interfacial Water Structure: Combining Molecular Dynamics Simulations with Convolutional Neural Networks
<p>Files for reproducing results from Kelkar et al. (JPCB 2020) - Predicting Hydrophobicity by Learning Spatiotemporal Features of Interfacial Water Structure: Combining Molecular Dynamics Simulations with Convolutional Neural Networks</p> <p> </p> <p>This folder contains simulations starter files and also plug-and-play datasets to test ML algorithms on molecular dynamics (MD) simulation data.</p> <p> </p> <p>All analysis scripts can also be found on GitLab on this link: https://gitlab.com/atharva-kelkar/kelkar_et_al_jpcb_2020</p>
Data from: Molecular data and distribution dynamics indicate a recent and incomplete separation of manakins species of the genus Antilophia (Aves: Pipridae) in response to Holocene climate change
To determine a hypothetical scenario that accounts for the diversification of the two species of the genus Antilophia, we conducted multilocus molecular comparisons and species distribution modeling for the two taxa, which have distinct male plumage coloration patterns and allopatric geographic distributions, despite the high degree of genetic similarity indicated by recent studies. Three mitochondrial and three nuclear fragments were analyzed. The results indicate clear differences in the genetic diversity of the two species, but with ample sharing of haplotypes in all the markers analyzed, reflecting the absence of reciprocal monophyly, presumably due to the relatively recent and still incomplete separation of the two species. The paleoclimatic distribution models, together with the observed genetic profile indicate a recent process of divergence by geographic isolation in the ancestral populations of the two species. This scenario coincides with the recent climatic events of the South American dry diagonal, which involves the gallery forests of the Cerrado biome and the cloud forest enclaves of the seasonal tropical dry forest of the Caatinga between the late Pleistocene and the mid Holocene.
Data from: Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change
Understanding the dynamics of molecular adaptation is a fundamental goal of evolutionary biology. While adaptation to constant environments has been well characterized, the effects of environmental complexity remain seldom studied. One simple but understudied factor is the rate of environmental change. Here we used experimental evolution with RNA viruses to investigate whether evolutionary dynamics varied based on the rate of environmental turnover. We used whole-genome next-generation sequencing to characterize evolutionary dynamics in virus populations adapting to a sudden versus gradual shift onto a novel host cell type. In support of theoretical models, we found that when populations evolved in response to a sudden environmental change, mutations of large beneficial effect tended to fix early, followed by mutations of smaller beneficial effect; as predicted, this pattern broke down in response to a gradual environmental change. Early mutational steps were highly parallel across replicate populations in both treatments. The fixation of single mutations was less common than sweeps of associated "cohorts" of mutations, and this pattern intensified when the environment changed gradually. Additionally, clonal interference appeared stronger in response to a gradual change. Our results suggest that the rate of environmental change is an important determinant of evolutionary dynamics in asexual populations.
Molecular Dynamics Study of the Vibrational Energy Exchange Between Nanodiamond and N-butylpyridinium Tetrafluoroborate Ionic Liquid
<p>Nanofluids are composed of certain nanoscale object immersed in the molecular or ionic liquid. Nanofluids generally exhibit higher thermal conductivities, as compared to conventional fluids. Therefore, they are interesting to applications, in which thermal conductivity is a cornerstone. Hereby, molecular dynamics simulations were used to study an energy exchange in one of the possible nanofluids: N-butylpyridinium tetrafluoroborate based solution of nanodiamonds. The data are given in the form of energy components versus time and atomistic trajectories versus time at a number of temperatures. The simulations were conducted in the constant energy ensemble to avoid efects of temperature coupling and pressure coupling. The dataset possesses both research and educational values.</p>
Datasets associated with the manuscript "Discovering SARS-CoV-2 neoepitopes and the associated TCR-pMHC recognition mechanisms by combining single-cell sequencing, deep learning, and molecular dynamics simulation techniques"
<p>meta_data_TCR-pMHC_from_STCRDab.tsv, TCR-pMHC structures used for contacts analysis.</p><p>tcr_gliph_input_sars2.tsv, input files (TCR sequences and related information) used for clustering TCRs targeting SARS-CoV-2 epitopes and epitope-unknown TCRs.</p><p>tcr_gliph_input_non-sars2.tsv, input files used for clustering TCRs targeting non-SARS-CoV-2 epitopes and epitope-unknown TCRs.</p><p>tcr_gliph_output*, output files from the GLIPH software, including the recognized TCR clusters by GLIPH (convergence-group.txt), the linkage information of TCR clusters (clone-network.txt), and the recognized motif in TCR clusters (kmer.txt).</p><p>md_trajs.tar, structures and MD simulation trajectories of TCR-614-pMHC and TCR-204-pMHC complexes.</p>
Molecular dynamics simulations of BmGtsf1L peptide interacting with eTD1 of BmVreteno
<p>AF-eTD1 of BmVreteno and the ten last residues of BmGtsf1L.</p><p>GRO file and files for 10 simulations runs. Processed XTC files. </p>
Molecular dynamics initialization files to reproduce simulations in "Anillin-Related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study"
<p>Molecular dynamics initialization files to reproduce simulations in "Anillin-Related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study" by Aaron R. Hall, Yeol Kyo Choi, Wonpil Im, and Dimitrios Vavylonis, Structure (2024) https://doi.org/10.1016/j.str.2023.11.010</p>
A LA-BTC MOF AS A SENSOR ELEMENT OF AN ELECTRONIC NOSE FOR SELECTIVE ADSORPTION OF BIOMARKERS OF DISEASES: MOLECULAR DYNAMICS SIMULATIONS OF ADSORPTION
<p>The MD trajectories calculated for all the La-BTC MOF-biomarker simulation systems </p>
Active learning molecular dynamics-assisted insights into ultralow thermal conductivity of two-dimensional covalent organic frameworks
<p>This is a training sets for monolayer COF-5, which could be used for NEP trainging.</p>
Dissecting the chiral recognition of TLR4/MD2 with Neoseptin-3 enantiomers by molecular dynamics simulations
Open the record for dataset details and reuse information.
Figure 3 from: Musfiroh I, Megawati G, Diah Herawati DM, Nama Putra O, Sylvia Nurrasjid E (2023) Molecular dynamic of omega-3 compounds as an anti-obesity agent into GPR-120 receptor. Pharmacia 70(4): 1541-1548. https://doi.org/10.3897/pharmacia.70.e115501
Figure 3 A. Visualization of interactions between docosahexaenoic acid and receptors (GPR120 (4GRV)) and B. Visualization of molecular docking between the receptor GPR120 (4GRV) and docosahexaenoic acid.
Figure 2 from: Musfiroh I, Megawati G, Diah Herawati DM, Nama Putra O, Sylvia Nurrasjid E (2023) Molecular dynamic of omega-3 compounds as an anti-obesity agent into GPR-120 receptor. Pharmacia 70(4): 1541-1548. https://doi.org/10.3897/pharmacia.70.e115501
Figure 2 A. Visualization of interactions between Neurotensin 8–13 and receptors (4GRV) and B. Visualization of molecular docking between the receptor 4GRV and natural ligand.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.