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MD simulation trajectory of POPE bilayer and related files

Simulation trajectory pre-equiblirated POPE bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2021.2 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-1000 ns, and we have disregarded the first 100 ns in our analysis. The system in the trajectory consists of 128 POPE and 6400 water molecules. Temperature 310 K, pressure 1 bar. Publication: <a href="https://doi.org/10.1016/j.bbamem.2022.183961">https://doi.org/10.1016/j.bbamem.2022.183961</a>

opencc-by-4.0Aug 2022View details →

MD simulation trajectory of SDPE bilayer and related files

Simulation trajectory pre-equiblirated SDPE bilayer and related files from all-atom molecular dynamics simulations. Simulations have been performed with GROMACS-2021.2 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-1000 ns, and we have disregarded the first 100 ns in our analysis. The system in the trajectory consists of 128 SDPE and 6400 water molecules. Temperature 310 K, pressure 1 bar. Publication: <a href="https://doi.org/10.1016/j.bbamem.2022.183961">https://doi.org/10.1016/j.bbamem.2022.183961</a>

MD simulation trajectory of POPC/DOG (18.75 mol%) bilayer and related files

Simulation trajectory pre-equiblirated POPC/DOG bilayer and related files from all-atom molecular dynamics simulations. The system contains 18.75mol% DOG. Simulations have been performed with GROMACS-2021.2 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-1000 ns, and we have disregarded the first 100 ns in our analysis. The system in the trajectory consists of 104 POPC, 24 DOG and 6400 water molecules. Temperature 310 K, pressure 1 bar. Publication: <a href="https://doi.org/10.1016/j.bbamem.2022.183961">https://doi.org/10.1016/j.bbamem.2022.183961</a>

MD simulation trajectory of POPE/CHOL (18.75 mol%) bilayer and related files

Simulation trajectory pre-equiblirated POPE/CHOL bilayer and related files from all-atom molecular dynamics simulations. The system contains 18.75mol% CHOL. Simulations have been performed with GROMACS-2021.2 with Lipid17 forcefield and TIP3P water model. The trajectory is 0-1000 ns, and we have disregarded the first 100 ns in our analysis. The system in the trajectory consists of 104 POPE, 24 CHOL and 6400 water molecules. Temperature 310 K, pressure 1 bar. Publication: <a href="https://doi.org/10.1016/j.bbamem.2022.183961">https://doi.org/10.1016/j.bbamem.2022.183961</a>

opencc-by-4.0Jul 2022View details →

LLZO Simulation Trajectories

Simulation trajectories (in xyz/gro/xtc format) at a range of temperatures of LLZO (from 500 K to 800 K and 1000 K), produced using MetalWalls (doi: 10.21105/joss.02373) and converted to gro format.

opencc-by-4.0Feb 2023View details →

LAMMPS trajectories for "The disordered N-terminal tail of SARS CoV-2 Nucleocapsid protein forms a dynamic complex with RNA"

LAMMPS trajectory data for: The disordered N-terminal tail of SARS CoV-2 Nucleocapsid protein forms a dynamic complex with RNA Jasmine Cubuk1,2, Jhullian J. Alston1,2, J. Jeremías Incicco1,2, Alex S. Holehouse1,2, Kathleen B Hall1, Melissa D. Stuchell-Brereton1,2, Andrea Soranno1,2,* 1Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110, Saint Louis, MO, USA 2Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA Corresponding author: Andrea Soranno (soranno@wustl.edu) Questions about simulations: Alex Holehouse (alex.holehouse@wustl.edu) Preprint link: <a href="https://doi.org/10.1101/2023.02.10.527914">https://doi.org/10.1101/2023.02.10.527914</a> GitHub link to simulation info: <a href="https://github.com/holehouse-lab/supportingdata/tree/master/2023/cubuk_2023">https://github.com/holehouse-lab/supportingdata/tree/master/2023/cubuk_2023</a> Funding: This research was supported by the NIH National Institute on Allergic and Infectious Diseases with R01AI163142 (to A.S., A.S.H.) and by the NIH National Cancer Institute F99CA264413 (to J.J.A.).

Correlates of protection and viral load trajectories in omicron breakthrough infections in triple vaccinated healthcare workers

Source data to figure 2-S1 and table S1 in manuscript entitled Correlates of protection and viral load trajectories in omicron breakthrough infections in triple vaccinated healthcare workers, Nature Communications, 2023.

opencc-by-4.0Dec 2022View details →

Single-cell RNA sequencing of Sox17-expressing lineages reveals distinct gene regulatory networks and dynamic developmental trajectories

Two seurat objects contains single-cell RNA sequencing data that captures Sox17-expressing lineages during embryogenesis. sox17_integrated_Figure2B.rds : This is a seurat object that contains single-cell RNA sequencing data from integration of GFP+ cells produced from Sox17GFPCre allele marking cells that currently express Sox17 or short-term progeny of Sox17-expressing progenitors and TdTomato+ cells produced from R26LSL.TdTomato reporter allele in the presence of Sox17GFPCre marking long-term progeny of Sox17-expressing progenitors. Inferred cell types in this seurat object reflects Figure 2B in the article. sox17_Prox1_endoderm_Figure5A.rds : This is a seurat object that contain single-cell RNA sequencing data from integration of Sox17- and Prox1-expressing endoderm dataset. Prox-1 expressing endoderm data is from the Willnow et al. Nature(2021). Inferred cell types in this seurat object reflects Figure 5A in the article.

opencc-by-4.0Jun 2022View details →

Air parcel trajectories dataset based on modeling of 16 deep convective clouds in the Amazon.

The dataset contains trajectories of 16 deep convective cloud air parcels simulated with MIMICA code based on soundings retrieved over Manaus (Latitude: -3.1, Longitude: -60.0) during the wet season from April 1 until April 14, 2020 at 00 and 12 UTC.   Parcel data contains values for coordinate (X, Y, Z), velocity components (U, V, W), potential temperature (PTIL), total water content (QT), water vapor (QV), condensate density (QC), precipitation density (QR), net precipitation change (QR_FLUX), relative humidity (RH), buoyancy (BUOY), temperature (T), pressure (P), resolved TKE (KRES), SGS TKE (SGS_TKE), turbulent diffusion (TDIFF) are provided for each parcel at every time step of the simulation.

opencc-by-4.0Apr 2023View details →

Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees: Source Data

Source Data file for the article "Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees"

FEP benchmark CDK8 FEP+ fmp and trajectory files

Full FEP+ fmp file and related trajectory files for CDK8 FEP+ calculations related to dataset https://github.com/MCompChem/fep-benchmark

opencc-by-4.0Apr 2023View details →

Fast Trajectory End-Point Prediction with Event Cameras for Reactive Robot Control

If you use any of this data, please cite the following publication: @inproceedings{monforte2023fast,   title={Fast Trajectory End-Point Prediction with Event Cameras for Reactive Robot Control},   author={Monforte, Marco and Gava, Luna and Iacono, Massimiliano and Glover, Arren and Bartolozzi, Chiara},   booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},   pages={4035--4043},   year={2023} } Event-based datasets of synthetic and real trajectories of a bouncing ball. The synthetic trajectories were obtained converting frames taken using Unreal Engine to events. The ground truth is provided along with objects and camera settings. The real trajectories wer dumped from a real event camera located in front of the robot workspace. To import .log files containing events, we suggest <a href="https://github.com/event-driven-robotics/bimvee">bimvee</a> Python library. Specifically use the functions to import .log files: data = importIitYarpBinaryDataLog(filePathOrName=input_path)

FEP benchmark TNKS2 FEP+ fmp and trajectory files

Full FEP+ fmp file and related trajectory files for TNKS2 FEP+ calculations related to dataset https://github.com/MCompChem/fep-benchmark

FEP benchmark EG5 FEP+ fmp and trajectory files

Full FEP+ fmp file and related trajectory files for EG5 FEP+ calculations related to dataset https://github.com/MCompChem/fep-benchmark

FEP benchmark CMET FEP+ fmp and trajectory files

Full FEP+ fmp file and related trajectory files for CMET FEP+ calculations related to dataset https://github.com/MCompChem/fep-benchmark

FEP benchmark HIF2A FEP+ fmp and trajectory files

Full FEP+ fmp file and related trajectory files for HIF2A FEP+ calculations related to dataset https://github.com/MCompChem/fep-benchmark

FEP benchmark SYK FEP+ fmp and trajectory files

Full FEP+ fmp file and related trajectory files for SYK FEP+ calculations related to dataset https://github.com/MCompChem/fep-benchmark

opencc-by-4.0May 2023View details →

All-atom DOPC + %10 Cholesterol MD Trajectories

Contains 100 trajectories of all-atom MD simulation of a bilayer membrane containing DOPC with %10 cholesterol at 30C. Each NC trajectory file corresponds to 10ns. The force-field used is CHARMM36. A PDB structure file is included.

opencc-by-4.0May 2023View details →

MD trajectories for "Kinetic barrier to enzyme inhibition is manipulated by dynamical local interactions in E. coli DHFR"

Dihydrofolate reductase (DHFR) is an important drug target and a highly studied model protein for understanding enzyme dynamics. DHFR’s crucial role in folate synthesis renders it an ideal candidate to understand protein function and protein evolution mechanisms. In this study, to understand how a newly proposed DHFR inhibitor, 4’-deoxy methyl trimethoprim (4’-DTMP), alters evolutionary trajectories, we studied interactions that lead to its superior performance over trimethoprim (TMP). To elucidate the inhibition mechanism of 4’-DTMP, we first confirmed, both computationally and experimentally, that the relative binding free energy cost for the mutation of TMP and 4’-DTMP are the same, pointing to the origin of the characteristic differences to be kinetic rather than thermodynamic. We then employed an interaction-based analysis by focusing first on the active site, then on the whole enzyme. We confirmed that the polar modification in 4’-DTMP induces additional local interactions with the enzyme, particularly the M20 loop. These changes are propagated to the whole enzyme as shifts in the hydrogen bond networks. To shed light on the allosteric interactions, we support our analysis with network-based community analysis and show that segmentation of the loop domain of the inhibitor-bound DHFR must be avoided by a successful inhibitor.