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393 results for “Molecular dynamics simulations”
Identification of Potential JNK3 Inhibitors Through Virtual Screening, Molecular Docking And Molecular Dynamics Simulation as Therapeutics for Alzheimer's Disease
<p>Alzheimer's disease (AD) is a complex neurological disorder without effective treatment. One factor in its development is c-Jun N-terminal kinases (JNKs), a type of protein related to brain function. JNK3, found mainly in the brain, contributes to AD by promoting brain abnormalities. Current research aims to create new JNK3 inhibitors for AD treatment using a virtual screening method. A database of compounds was filtered, and five potential compounds were identified with better scores than a reference. These compounds underwent simulations and energy calculations, showing stability and potential as JNK3 inhibitors.</p>
Molecular dynamics simulation trajectories for the GB99dms implicit solvent force field
<p>Molecular dynamics simulation trajectories used in training and validating the GB99dms implicit solvent protein force field. See the paper:</p> <ul> <li>Greener JG. Differentiable simulation to develop molecular dynamics force fields for disordered proteins, <a href="https://doi.org/10.1039/D3SC05230C" target="_blank" rel="noopener">Chemical Science</a> 15, 4897-4909 (2024)</li> </ul> <p>For more information, including structure files for these trajectories, see https://github.com/greener-group/GB99dms.</p>
Molecular dynamics simulations of hyaluronan octamer–tetrapeptide mixtures
<p><strong>To cite:</strong> Riopedre-Fernandez, M.; Biriukov, D.; Dračínský, M.; Martinez-Seara, H. Hyaluronan-arginine enhanced and dynamic interaction emerges from distinctive molecular signature due to electrostatics and side-chain specificity. Carbohydr. Polym. 2024, 325, 121568. DOI: <a href="https://doi.org/10.1016/j.carbpol.2023.121568">10.1016/j.carbpol.2023.121568</a></p> <p>MD simulations of hyaluronan octamer (HA8) with tetrapeptides. Simulation files and molecular topologies are provided.</p> <p>Tetrapeptides simulated: tetraarginine (R4), tetralysine (K4), tetraalanine (A4), tetraproline (P4), tetraglycine (G4), arginine-lysine-arginine-lysine (RKRK), and tetraglutamic acid (E4).</p> <p>Two force fields were compared: CHARMM (version charmm36-jul2020.ff.tgz from <a href="http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs">http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs</a>) and prosECCo75 (<a href="https://gitlab.com/sparkly/prosecco/prosECCo75">https://gitlab.com/sparkly/prosecco/prosECCo75</a>).</p> <p>Each simulation contained one hyaluronan polymer, one tetrapeptide, CHARMM-specific TIP3P water, and potassium counterions (standard "K" model in CHARMM and "K_s" model in prosECCo75) when necessary.</p> <p>We also additionally performed: (i) reference simulations with only hyaluronan octamer and potassium counterions; (ii) reference simulations with only R4 or K4 peptide and chloride counterions; (iii) simulations with two peptides (R4, K4, or G4) and two hyaluronan octamers.</p> <p>Simulations were done in Gromacs.</p> <p>Length - at least 1 µs, prolonged till 2 µs for prosECCo75 systems with R4, K4, or G4 peptides.</p> <p>Temperature - 300 K.</p> <p>For peer-reviewing process, extracted PDB configurations (a configuration every 10 ns of 2 μs simulations excluding the first 100 ns of equilibration) from selected systems were separately uploaded to <a href="http://doi.org/10.5281/zenodo.8423276">http://doi.org/10.5281/zenodo.8423276</a></p>
Introduction to HPC: molecular dynamics simulations with GROMACS: log files
<p>Introduction to HPC: molecular dynamics simulations with GROMACS: log files corresponding to the exercises 1.X 2.X 3.X</p>
Molecular dynamics simulations of hyaluronan octamer–tetrapeptide mixtures (PDB configurations)
<p>Extracted PDB configurations from MD simulations of hyaluronan octamer (HA8) with R4 and K4 tetrapeptides. Simulated explicit water was removed for clarity.</p> <p>See <a href="https://doi.org/10.5281/zenodo.8028600">10.5281/zenodo.8028600</a> for more details about simulated systems.</p>
Introduction to HPC: molecular dynamics simulations with GROMACS: output files - Devana
<p> Introduction to HPC: molecular dynamics simulations with GROMACS: log files corresponding to the exercises 1.1, 1.2 2.1 3.1 and 3.2</p>
Electrofreezing of liquid water at ambient conditions - trajectories from ab initio molecular dynamics simulations
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Data from: All-atom molecular dynamics simulation and rate calculation for norepinephrine binding beta adrenergic receptor
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Data from: programming co-assembled peptide nanofiber morphology via anionic amino acid type: insights from molecular dynamics simulations
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Molecular Dynamics Simulations and associated data for: Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases
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Molecular mechanism underlying SNARE-mediated membrane fusion enlightened by all-atom molecular dynamics simulations
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A lever hypothesis for Synaptotagmin-1 action in neurotransmitter release and Studies of Synaptotagmin-1 action by all-atom molecular dynamics simulations
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All-atom molecular dynamics simulations of synaptic vesicle fusion I: a glimpse at the primed Synaptotagmin-SNARE-complexin complex
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Data from: Elucidating the impact of red blood cell membrane components on melittin-induced pore formation with molecular dynamics simulations
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Molecular dynamics simulations in: High-resolution structures with bound Mn2+ and Cd2+ map the metal import pathway in an Nramp transporter
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Molecular dynamics simulation data of ELIC in nanodiscs
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Molecular dynamics simulation files for: a molecular machine efficiently drives glycosaminoglycan assembly and secretion for osteoarthritis therapy
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Molecular dynamics simulation of Conus textile conotoxin Txd13 in complex with a3b2, a3b4, a6b2 or a6b4 nAChR subtypes.
<p>This folder contains the coordinate and parameter files used to run molecular dynamics simulations of the toxin Txd13 (sequence GCCSNPPCIANPMC) in complex with four nicotinic acetylcholine receptor (nAChR) subtypes: a3b2, a3b4, a6b2 and a6b4 nAChRs. For each system several files are provided:</p> <p>1) an homology model that was used as a starting conformation is provided (eg 'a3b2_txd13.B99990023.pdb'),<br> 2) an Amber Parm7 topology file (eg 'a3b2_txd13_0023.prmtop'),<br> 3) a trajectory files containig 1250 frames extracted from a 100 ns molecular dynamics simulation (eg 'a3b2_txd13_0023_md_smaller.nc') created using pmemd from the Amber 18 package,<br> 4) the log file of this simulations (eg 'a3b2_txd13_0023_md.log'), and<br> 5) the coordinate file representing the minimized verion of the centroid frame of each simulation (with water and ions removed for conveniance) (eg 'a3b2_txd13_0023_md_centroid_min_nowat.pdb')</p> <p>The parameters used for the molecular dynamics simulations are provided in the 'md.in' file.</p> <p>All the text files have been compressed in the 'xz' format</p>
Files for Molecular Dynamics Simulation of COSAN
<p>Topology file (.top), force field parameters file (.prm) and coordinate file (.pdb) for Molecular Dynamics Simulations of COSAN molecule compatible with CHARMM force field. Files based on the parameters reported in:</p> <p>D.C. Malaspina, C. Viñas, F. Teixidor, J. Faraudo "Atomistic Simulations of COSAN: Amphiphiles without a Head-and-Tail Design Display “Head and Tail” Surfactant Behavior", Angewandte Chemie International Edition Vol 59(8), Pages 3088-3092 (2020)</p> <p>DOI: <a href="https://doi.org/10.1002/anie.201913257">10.1002/anie.201913257</a></p>
Replica exchange molecular dynamics simulation data of designed β-hairpins (implicit solvent, AMBER ff99SB-ildn-nmr)
<p>Raw REMD simulation data (protein only) of designed β-hairpins. AMBER ff99SB-ildn-nmr and implicit solvent model is used. More details can be found in this paper: </p> <p>Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132"><em>Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</em></a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620</p>
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Allen Brain Atlas
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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.