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691 results for “Molecular dynamics”

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zenodo36/100

Revisiting the allosteric regulation of sodium cation on the binding of adenosine at the human A2A adenosine receptors: insights from Supervised Molecular Dynamics (SuMD) simulations.

SuMD trajectories Videos   Video 1: Sodium binding pathway on the antagonist-bound state of A2AR. The video is composed of four synchronized and animated panels that depict the molecular trajectory obtained by the SuMD simulation considering different aspects of the simulation. The time evolution is reported in a nanosecond. In the first panel (upper-left), the molecular representation of the macromolecular system is shown. The A2AR antagonist-bound state backbone is represented by the ribbon style (cyan colour) and the residues within 4 Å of sodium ion during the entire simulation are dynamically shown. Na+ is rendered showing its VdW volume in yellow. In the second panel (upper-right), the dynamic distance of sodium center of mass (CM) from the A2AR allosteric binding site during the trajectory is reported. In the third panel (lower-left), the MMGBSA energy profile is reported. The animated red circle highlights the value of the corresponding frame. The trend is depicted by a continuous black line obtained by smoothing the raw data (grey circles) using a Bezier curve procedure. In the fourth panel (lower-right) cumulative electrostatic interactions are reported for the 15 A2AR residues most contacted by sodium during the whole simulation.   Video 2: Adenosine different binding pathways collection on the two relevant states of A2AR The video is composed of two panels, which summarizes the recognition process of the adenosine agonist, sampled by means of the supervised molecular dynamics methodology, in the two pharmacologically relevant states of the receptor. In particular, on the right side are shown simultaneously all ten replicas collected starting from the agonist-bound conformation of the A2AR (pink ribbon). The meta-binding site located at the level of the ECL2 and the orthosteric binding site were highlighted. On the left side are represented simultaneously all ten replicas collected starting from the antagonist-bound conformation of the A2AR (cyan ribbon). The meta-binding site located at the level of the ECL2 and the extracellular receptor vestibule were highlighted.   Video 3: Adenosine binding pathway on the agonist-bound state of A2AR. The video is composed of four synchronized and animated panels that depict the molecular trajectory obtained by the SuMD simulation considering different aspects of the simulation. The time evolution is reported in a nanosecond. In the first panel (upper-left), the molecular representation of the macromolecular system is shown. The A2AR agonist-bound state backbone is represented by the ribbon style (pink colour) and the residues within 4 Å of sodium ion during the entire simulation are dynamically shown. Adenosine molecule is rendered by orange carbon atoms and by a transparent surface. In the second panel (upper-right), the dynamic distance of agonist center of mass (CM) from the A2AR allosteric binding site during the trajectory is reported. In the third panel (lower-left), the MMGBSA energy profile is reported. The animated red circle highlights the value of the corresponding frame. The trend is depicted by a continuous black line obtained by smoothing the raw data (grey circles) using a Bezier curve procedure. In the fourth panel (lower-right) cumulative electrostatic interactions are reported for the 15 A2AR residues most contacted by adenosine during the whole simulation.

opencc-by-4.0Jun 2019View details →

zenodo36/100

Supervised Molecular Dynamics Movies from: Deciphering the molecular recognition mechanism of multidrug resistance Staphylococcus aureus NorA efflux pump using a Supervised Molecular Dynamics approach

Molecular Recognition pathway of Supervised molecular dynamic simulations of MdfA-CLM NorA-CPX and  NorA-CPX.

opencc-by-4.0Jul 2019View details →

zenodo36/100

Deciphering the molecular recognition mechanism of multidrug resistance Staphylococcus aureus NorA efflux pump using a Supervised Molecular Dynamics approach.

Legend of Movie-S1 The Movie is composed by four synchronized and animated panels that show different aspects of the SuMD simulation. The time evolution is reported in nanosecond. In the first panel (upper left), the molecular representation of the system is shown. The MdfA backbone is represented by the new cartoon style (cyan). The CLM is shown in yellow and by a transparent surface. The protein residues within 3 Å from the ligand are made explicit by a stick representation. In the second panel (upper-right), the CM-distance between the protein and the ligand centers of mass is reported. In the third panel (lower left), the MMGBSA energy profile is reported. In the fourth panel (lower-right) cumulative electrostatic interactions are reported for the 15 MdfA residues most contacted by CLM during the whole simulation.   Legend of Video-S2 The Movie shows the SuMD trajectory of CLM on MdfA compared to the CLM crystallographic pose. MdfA is represented in cyan new cartoon transparency. The crystallographic pose is showed in yellow while the experimental one in light green. At 16.69 ns a RMSD value of 1.77 Å is highlighted.   Legend of Video-S3 The Movie is composed by four synchronized and animated panels that show different aspects of the SuMD simulation. The time evolution is reported in nanosecond. In the first panel (upper left), the system is shown. The NorA backbone is represented by the new cartoon style (red) and the protein residues within 3 Å of CPX are showed in stick. CPX is rendered by a green stick. In the second panel (upper-right), the distance between the centre of mass of the ligand and the protein during the trajectory is reported. In the third panel (lower left), the MMGBSA energy profile is reported. In the fourth panel (lower-right) cumulative electrostatic interactions are reported for the 15 NorA residues most contacted by CPX during the whole SuMD trajectory. It is important to note that the following video has a duration that is half of the simulation of SuMD. However, this straid does not alter the description of the trajectory performed by the ligand.   Legend of Video-S4 The Movie depicts the clustering analysis of CPX during the whole SuMD simulation. The NorA protein is shown in red new cartoon transparency. CPX is rendered by a light-green stick and by a transparent surface. The spheres are shown in 7 different colours, according to the different clusters. Each sphere dimension is in according to the cluster dimensions. After a first recognition site, the ligand conformations are clustered in different sites of the NorA channel. It is important to note that the following video has a duration that is half of the simulation of SuMD. However, this straid does not alter the description of the trajectory performed by the ligand.

opencc-by-4.0Aug 2019View details →

zenodo36/100

Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R111A) with arachidonic acid (POSES 1-3)

Description of files in this dataset: MD_mutR111A_CYP2J2_AA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the R111A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)

opencc-by-4.0Oct 2019View details →

zenodo36/100

Molecular dynamics simulations of the interaction of the double mutant human CYP2J2 (R117A and R111A) with arachidonic acid (POSES 4-6)

Description of files in this dataset: MD_mutR111A_R117A_CYP2J2_AA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the double R111A + R117A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage

opencc-by-4.0Oct 2019View details →

zenodo36/100

Speciation data for "Pressure-induced coordination changes in a pyrolitic silicate melt from ab initio molecular dynamics simulations"

With ab initio molecular dynamics simulations on pyrolite melt, we examine the detailed changes in elemental coordination as a function of pressure and temperature. We consider the average coordination as well as the proportion and distribution of coordination environments at pressures and temperatures encompassing the conditions at which molten silicates may exist in present-day Earth and those of the Early Earth's magma ocean. At ambient pressure and 2000 K, we find that the average coordination of cations with respect to oxygen is 4.0 for Si-O, 4.0 for Al-O, 3.7 for Fe-O, 4.6 for Mg-O, 5.9 for Na-O and 6.2 for Ca-O. Although the coordination for iron with respect to oxygen is underestimated, the coordination number for all other cations are consistent with experiments. At the base of the upper mantle (~15 GPa and 2000 K), the average coordination for Si-O remains at 4.0, but increases to 4.1 for Al-O, 4.2 for Fe-O, 4.9 for Mg-O, 8.0 for Na-O and 6.8 for Ca-O. The coordination environment for Na-O remains approximately constant up to core-mantle boundary conditions (135 GPa and 4000 K), but increases to about 6 for Si-O, 6.5 for Al-O, 6.5 for Fe-O, 8 for Mg-O, 9.5 for Ca-O. Our results have implications for melt properties, such as viscosity, transport coefficients, thermal conductivities and electrical conductivities, and will help interpret experimental results on silicate glasses. Detailed speciation statistics for pyrolite melt were determined using ab initio molecular dynamics simulations with the Vienna Ab Initio Simulation Package (VASP) (Kresse and Furthmuller, 1996). Simulations were performed with a time step of 0.5-2 femtoseconds for 10-50 picoseconds, depending on the temperature and density. The composition of the Bulk Silicate Earth was modeled with a pyrolite melt with the stoichiometry NaCa2Fe4Mg30Al3Si24O89. Bond distances were determined from the pair distribution functions, which describe the probability of finding an atom type at a given distance from the reference atom. We used the first peak in the pair distribution function to approximate the average bond length; the distance at which the first minimum occurs marks the radius of the first coordination sphere of atoms that are directly bonded to the reference atom. We used this value to define the bond criterion between two atom types. Additional computational details can be found in the manuscript.

opencc-by-4.0Nov 2019View details →

zenodo36/100

Molecular dynamics simulation input files: Dynamics of amphiphilic poly($\varepsilon$-caprolactone) micelles with doxorubicin and transition temperature predictions using all-atom molecular dynamics simulation

The files uploaded contain the input files for simulations: 1) P10_Solv: Input files for drug-free micelles. 2) Micelle_Solv: Input files for drug-loaded micelles.

opencc-by-4.0Aug 2024View details →

zenodo36/100

Contrasting Views of the Electric Double Layer in Electrochemical CO2 Reduction: Continuum Models vs Molecular Dynamics (data for figures)

This is the data used to create the figures in the article: <h4>Contrasting Views of the Electric Double Layer in Electrochemical CO2 Reduction: Continuum Models vs Molecular Dynamics</h4> <div>Evan Johnson and Sophia Haussener</div> <div>The Journal of Physical Chemistry C 2024 128 (25), 10450-10464</div> DOI: 10.1021/acs.jpcc.4c03469 See the file "Naming conventions" for the file names and column/row meanings.

opencc-by-4.0Aug 2023View details →

zenodo36/100

Effect of Solar Wind and Micrometeoroid Impact on the Lunar Water Cycle: A Molecular Dynamics Study

<ul> <li>.txt files contain the data used to plot the hydrogen distributions.</li> <li>.csv files contain the data used to plot the temperature distribution graphs.</li> </ul>

opencc-by-4.0Aug 2024View details →

zenodo36/100

Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations to Accurately Model Glycosaminoglycan Electrostatic Interactions

To cite and for more details: Riopedre-Fernandez et al. J. Chem. Inf. Model. 2024, 64 (18), 7122–7134. DOI: <a href="https://doi.org/10.1021/acs.jcim.4c00981">https://doi.org/10.1021/acs.jcim.4c00981</a> The dataset includes molecular dynamics simulations of sulfated saccharides and their sulfated analogs in the presence of calcium cations in aqueous solution. Several force field parameter sets were compared (CHARMM36, GLYCAM06, AMOEBA, Drude) and new have been developed (prosECCo75 and GLYCAM-ECC75). The uploaded files contain the following simulation input files or/and simulation trajectories: 1) Sulfated_Molecules_Umbrella_Sampling_AIMD: Umbrella sampling ab initio molecular dynamics simulations of calcium-methylsufate and calcium N-methylsulfamate ion pairs in water. 2) Sulfated_Molecules_Umbrella_Sampling_FFMD: Umbrella sampling force field molecular dynamics simulations of calcium-methylsufate and calcium N-methylsulfamate ion pairs in water. 3) Sulfated_Molecules_AWH_FFMD: Accelerated weight histogram force field molecular dynamics simulations of calcium interacting with both methylsufate and N-methylsulfamate in water. 4) Disaccharides_FFMD: Unbiased force field molecular dynamics simulations of calcium-sulfated disaccharide aqueous solutions. UPD. Version 2.0 has updated one of the disaccharide-containing simulations (GLYCAM06, N-sulfation) due to incorrect calcium LJ parameters in the original upload.

opencc-by-4.0Aug 2024View details →

zenodo36/100

Molecular dynamics of free HMO1 model and HMO1 bound to the DNA

<div>Files:</div> <div>1. Initial models of free HMO1 and HMO1 bound to DNA.</div> <div>2. 1 µs MD trajectories of free HMO1 and HMO1 bound to DNA.</div> <div>3. MD protocol for GROMACS</div>

opencc-by-4.0Sep 2024View details →

zenodo36/100

Molecular dynamics simulations of RNA Pol I closed complex in WT and with modifications to DNA base pairs -27 and -28

The starting structure for the modelling was cryo-EM based structure of S. cerevisiae pre-initiation complex, showing Pol I, RRN3 and CF bound on a rDNA promoter at 2.90 Å resolution. This structure (‘RNA Polymerase I closed conformation 2’; accession code: 6RQL) was downloaded from the PDB database and prepared using the Protein Preparation Workflow of Maestro with default settings. This included filling in missing sidechains, optimizing hydrogen bonds and protonation using PROPKA at pH 7.4, deleting water molecules >5Å from the heteroatoms and a short energy minimization using OPLS4 force field. The initial structures for the complexes with DNA mutations were constructed from this pre-processed structure by manually mutating the base pairs at position -28 or -27 of the rDNA promoter from C·G to A·T (tDNA·ntDNA) and from A·T to C·G, respectively. MD simulations (3*80 ns/system) were conducted with Desmond using default parameters from Schrödinger Suite version 2024-1 on the CSC (IT Center for Science, Finland) supercomputer Puhti.

opencc-by-4.0Oct 2024View details →

zenodo36/100

Trajectories of Microsecond Molecular Dynamics Simulations of the Orexin Receptor 2 System with Lemborexant

This data set contains psf files and trajectories (.dcd files) of the performed simulations for the orexin receptor 2 system: 1) the orexin type 2 receptor (OX2R) in complex with lemborexant, three replicas

opencc-by-4.0Nov 2024View details →

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Trajectories of Microsecond Molecular Dynamics Simulations of the Orexin Receptor 2 System with Compound 1

opencc-by-4.0Nov 2024View details →

zenodo36/100

Molecular Dynamics Trajectories for GPR6 without Ligand (ApoNoLig)

Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3. This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands. Please cite us if you find this data useful!

opencc-by-4.0Nov 2024View details →

zenodo36/100

Molecular Dynamics Trajectories for GPR6 with Ligand OLA

opencc-by-4.0Nov 2024View details →

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Molecular Dynamics Trajectories for GPR6 without Ligand (IagNoLig)

opencc-by-4.0Nov 2024View details →

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Project files provided as supporting information to the manuscript "How Communication Pathways Bridge Local and Global Conformations in an IgG4 Antibody: a Molecular Dynamics Study"

June 23, 2021 Thomas Tarenzi, Marta Rigoli and Raffaello Potestio ================================== The dataset contains the following folders: - contact_area_binding_site: files with the computed surface area, used for the calculation of the contact area between PD-1 and the antibody Fab (Fig. S41). - hbonds_ab-pd1: number of hydrogen bonds between the antigen and the antibody, for each holo cluster (Fig. S41). - mutual_information: matrices with the computed mutual information, for each pair of residues (Fig. S34, S35, S46). The folder contains also the generalized correlation coefficients (Fig. S43) and the correlation scores (Fig. 4, S44, S45), computed from the mutual informations. - networks: communities - for each cluster, each residue is assigned to a community within the interaction network (Fig. S32, S33). betweenness - the values of edge betweenness for each cluster (S30, S31). - output_clustering: each frame of the apo and holo simulations is assigned a cluster index, on the basis of the structural similarity (Fig. S4). - PAD: per-residue values of PAD parameter, for apo and holo systems (Fig. 3, S39). - PCA: principal component analysis for each conformational cluster (Section S2.1). - representative_structures: representative structures for each conformational cluster (Fig. 2). - r_gyr_antibody: radii of gyration of the antibody, for each cluster (Fig. 2). - r_gyr_hinge: radii of gyration of the sole hinge segment, for each cluster (Fig. S36). - RMSD_antibody: distributions of the root-mean-square deviation of the antibody, for each cluster (Fig. S5).  - RMSD_antigen: root-mean-square deviation of the antigen PD-1, for each cluster (Fig. S42). - RMSD_binding_site: distributions of the root-mean-square deviation of the residues belonging to the paratope, for each cluster (Fig. S40, S47). - RMSD_matrix: root-mean-square deviation between structures belonging to different pairs of clusters (Fig. S9). - rmsf_antigen: root-mean-square fluctuation of the antigen PD-1, for each cluster (Fig. S42). - rmsf_hinge: difference between the total root-mean-square fluctuations of the two hinge segments, for each cluster (Fig. S38). - salt_bridge: distribution of distances between residues R979 and D1377 (Fig. 4). - sasa_domains: contact area between Fab and Fc antibody domains, for each cluster (Fig. S8). - sasa_hinge: solvent accessible surface area of each hinge segment, for each cluster (Fig. S37).

opencc-by-4.0Jun 2021View details →

zenodo36/100

Molecular Dynamics Simulation of MC-congeners in complex with PPP1 - Replicate 3

This data sets contains Molecular Dynamics (MD) Simulation files and analysis. Microcystin (MC) congeners were simulated in solvent (water) and in complex with protein phosphatase 1 (PPP1). MD Simulation was repeated for three times. This data is replicate 3 and related data sets are available. Please cite the original publication when using all or part of the data: S. Jaeger-Honz, J. Nitschke, S. Altaner, K. Klein, D. R. Dietrich, F. Schreiber:<a href="https://doi.org/10.1016/j.cbi.2021.109766"> Investigation of microcystin conformation and binding towards PPP1 by molecular dynamics simulation</a>. Chemico-Biological Interactions, 2021

opencc-by-4.0Jun 2021View details →

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Molecular Dynamics Simulation of MC-congeners in complex with PPP1 - Replicate 2

This data sets contains Molecular Dynamics (MD) Simulation files and analysis. Microcystin (MC) congeners were simulated in solvent (water) and in complex with protein phosphatase 1 (PPP1). MD Simulation was repeated for three times. This data is replicate 2 and related data sets are available. Please cite the original publication when using all or part of the data: S. Jaeger-Honz, J. Nitschke, S. Altaner, K. Klein, D. R. Dietrich, F. Schreiber:<a href="https://doi.org/10.1016/j.cbi.2021.109766"> Investigation of microcystin conformation and binding towards PPP1 by molecular dynamics simulation</a>. Chemico-Biological Interactions, 2021

opencc-by-4.0Jun 2021View details →

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Last verified 2026-04-30Open record

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abode-home-cage

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Last verified 2026-04-30Open record

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dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

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.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

OpenNeuro

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openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record