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50 results for “Enhanced sampling”
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- Part 3
<p>Trajectories and input files for the simulations of the Rbfox·pre-miR20b complex.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- PART 2
<p>Trajectories and input files of the simulations of the free pre-miR20b.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study-PART 7
<p>Simulations of the Rbfox*-miR20b and of the Rbfox-mir20b* complexes.</p>
MD simulations files for: Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning
<p>Here's a rephrased version of the README file:</p> <p>#### Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning</p> <p>**Authors:** Mingyuan Zhang, Hao Wu, Yong Wang</p> <p>This repository contains the official implementation for the paper "Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning" by Mingyuan Zhang, Hao Wu, and Yong Wang. Included are all trajectories from our MD simulations in the form of PLUMED COLVAR files, as well as all analysis scripts and files needed to replicate the results and figures presented in both the main text and Supporting Information (SI) of the paper.</p> <p>The paper features two examples: Ala2 and Ala10. For each, we have organized all the associated simulation files as they were during our automated simulation pipeline. The directory structure is the same for both examples. Here, we use Ala2, found in the `Ala2` folder, as an example:</p> <p>### Key Components</p> <p>- **Automated Pipeline Implementation:** The pipeline is implemented in `Ala2/7-adaptive-40ps/ala2.ipynb`. This implementation is ready to use once all required packages are installed, and gmx/gmx_mpi/plumed are callable within the notebook. After configuring the environment and specifying parameters like `gpu_id`, `ntomp`, and `n_sim` according to your hardware, running the blocks will replicate the entire pipeline.</p> <p>- **Analysis Scripts:** The scripts to replicate the results or figures from the main text or SI are organized in three files: `Ala2/7-adaptive-40ps/AdaptiveSamplingAnalysis.ipynb`, `Ala2/7-adaptive-40ps/compare_with_msm.ipynb`, and `Ala2/7-adaptive-40ps/opes/COLVAR/analysis.ipynb`.</p> <p>### Directory Structure</p> <p>Under the `Ala2` main directory, there are seven subdirectories:</p> <p>- **`Ala2/1-topol/`**: Contains files generated during system construction, including the final Gromacs topology file `topol.top`, which is necessary for running the automated simulation script.</p> <p>- **`Ala2/2-em/`, `Ala2/3-nvt/`, `Ala2/4-npt/`**: These directories store files generated during energy minimization and NVT/NPT equilibration. The `Ala2/4-npt/npt.gro` file is required to run the automated simulation script.</p> <p>- **`Ala2/mdp/`**: Contains all mdp files used, including `Ala2/mdp/md_detail.mdp`, which is necessary for running the automated simulation script.</p> <p>- **`Ala2/7-adaptive-40ps/`**: Contains all simulation and analysis scripts, along with files required to replicate the study related to the automated pipeline.</p> <p> 1. **`Ala2/7-adaptive-40ps/CV/`**: Stores all COLVAR files from adaptive sampling simulations.<br> <br> 2. **`Ala2/7-adaptive-40ps/opes/`**: Contains all files related to OPES simulations, including raw data for the final FES plots found in `Ala2/7-adaptive-40ps/opes/COLVAR/`. The script for replicating OPES and FES estimation figures is located in `Ala2/7-adaptive-40ps/opes/COLVAR/analysis.ipynb`.<br> <br> 3. **`Ala2/7-adaptive-40ps/figures/`**: Includes all original figures from the main text and SI, saved at 600 dpi.<br> <br> 4. **`Ala2/7-adaptive-40ps/traj_and_dat/`**: Stores all PLUMED `*.dat` files for the `DRIVER` utility in adaptive sampling simulations, a topology file `input.pdb` for PLUMED `MOLINFO`, and a topology file `seed_ref.pdb` for MDAnalysis adaptive sampling seed `*.gro` generation. Note that all `*.xtc` files from adaptive sampling were deleted to reduce the package size.<br> <br> 5. **Seed Index Files:** Seed indices for each round are stored as `Ala2/7-adaptive-40ps/round{i}_seed.txt`, necessary for figure replication.<br> <br> 6. **Automated Pipeline Notebook:** Implemented in `Ala2/ala2.ipynb`. Ensure that all imported packages are installed and gromacs (both gmx and gmx_mpi)/plumed can be called within the Jupyter notebook.<br> <br> 7. **Adaptive Sampling Analysis:** Scripts for analyzing adaptive sampling trajectories are found in `Ala2/AdaptiveSamplingAnalysis.ipynb`. This notebook contains scripts to replicate all figures related to adaptive sampling.<br> <br> 8. **MSM Comparison:** Analysis scripts for MSM comparison are located in `Ala2/compare_with_msm.ipynb`. This notebook contains scripts to replicate figures used for MSM/OPES comparison.</p> <p>- **`Ala2/8-adaptive-400ps/`**: Contains all simulation files (except xtc) for an additional adaptive sampling dataset computed for MSM comparison.</p> <p>### Contact Information</p> <p>We are continuing to test and improve the pipeline, so a tutorial is not yet available. Please feel free to reach out with any questions related to the implementation via email at mingyuanzhang@zju.edu.cn or by raising an issue on our GitHub page: https://github.com/yongwangCPH/papers/tree/main/2024/ALICE.</p>
AggMapNet: Enhanced and Explainable Low-Sample Omics Deep Learning with Feature-Aggregated Multi-Channel Networks
<p>This data contains the datasets used in the paper "AggMapNet: Enhanced and Explainable Low-Sample Omics Deep Learning with Feature-Aggregated Multi-Channel Networks", each folder is named by the dataset name in the paper</p>
Human Papillomavirus Self-sampling for Enhancing Cervical Screening During the War in Ukraine
ClinicalTrials.gov study NCT07275333. IPD Sharing: NO. Countries: 1. Publications: 1.
Koopman-based Control for Stochastic Systems: Application to Enhanced Sampling
Open the record for dataset details and reuse information.
Dataset for Label-free Surface Enhanced Raman Scattering (SERS) on Centrifugal Silver Plasmonic Paper (CSPP): a novel methodology for unprocessed biofluids sampling and analysis.
<p>This dataset contains all the spectra used in "Label-free Surface Enhanced Raman Scattering (SERS) on Centrifugal Silver Plasmonic Paper (CSPP): a novel methodology for unprocessed biofluids sampling and analysis". Data are available in 2 different formats:</p> <p>- a compressed archive ("Spectra.zip") with 5 folders ("Figure 1-5”) containing all the *.txt files used to generate the 5 figures in the original paper (1 file = 1 spectrum).</p> <p>- 5 single CSV files (“Figure-X_all-spectra-and-metadata.csv”) with all the spectra and metadata relative to a specific figure. The data are structured as follow, with each row being 1 spectrum, followed by metadata.</p>
Supplementary material 2 from: Swenson SJ, Eichler L, Hörren T, Kolter A, Köthe S, Lehmann GUC, Meinel G, Mühlethaler R, Sorg M, Gemeinholzer B (2022) The potential of metabarcoding plant components of Malaise trap samples to enhance knowledge of plant-insect interactions. Metabarcoding and Metagenomics 6: e85213. https://doi.org/10.3897/mbmg.6.85213
Table S2
Supplementary material 1 from: Swenson SJ, Eichler L, Hörren T, Kolter A, Köthe S, Lehmann GUC, Meinel G, Mühlethaler R, Sorg M, Gemeinholzer B (2022) The potential of metabarcoding plant components of Malaise trap samples to enhance knowledge of plant-insect interactions. Metabarcoding and Metagenomics 6: e85213. https://doi.org/10.3897/mbmg.6.85213
Table S1
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- PART 6
<p>Trajectories and input files of the simulations of the S151T Rbfox*·pre-miR20b* system.</p>
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study- PART 1
<p>Simulations of the Rbfox protein.</p> <p> </p>
Tretinoin synergistically enhances the antitumor effect of combined BRAF, MEK, and EGFR inhibition in BRAFV600E colorectal cancer [RKO samples]
GEO Series GSE269880. Homo sapiens. 4 samples. Type: Expression profiling by array.
Pomalidomide as an immune-enhancing agent in samples from people living with HIV
GEO Series GSE244148. Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing.
Super-enhancer H3K27ac CUT& Tag sequencing of six human gastric cancer tissue samples
GEO Series GSE275349. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Enhanced Reduced Representation Bisulfite Sequencing of BPH and control samples
GEO Series GSE123111. Homo sapiens. 23 samples. Type: Methylation profiling by high throughput sequencing.
Genome-wide chromatin interaction maps of enhancer-promoter and promoter-promoter contacts in 5 leiomyoma (MED12 G44 mutant) and 5 matched normal myometrium (WT) patient tissue samples.
GEO Series GSE128234. Homo sapiens. 10 samples. Type: Other.
Data from: Is Hydroides dianthus (Verrill, 1873) really a Mediterranean native? Increased sampling in the eastern United States reveals enhanced genetic diversity
<p>The introduction of non-indigenous species (NIS) is a significant threat to marine biodiversity, facilitated by vectors such as shipping and aquaculture. <em>Hydroides dianthus,</em> a tubicolous polychaete worm, is known for its biofouling capabilities, impacting both shipping and aquaculture. Traditionally, the east coast of the United States has been considered the native range of <em>H. dianthus</em>. However, previous studies have suggested the Mediterranean region as the species' true native range based on higher genetic diversity. This study aims to re-evaluate the genetic diversity patterns of <em>H. dianthus</em> on the east coast of the United States by expanding the cytochrome c oxidase I (COI) dataset currently available for the species. Samples were collected from various locations on the east coast and analyzed using DNA barcoding. The results revealed a three-fold increase in haplotype diversity on the east coast compared to previous findings. A hierarchical AMOVA indicated significant genetic structuring between the Mediterranean and U.S. populations (ϕST = 0.51, P < 0.05). Despite a higher genetic diversity in the Mediterranean, this study highlights the variability of genetic diversity estimates and the challenges in using such metrics to delineate native ranges. Factors such as multiple introductions, genetic drift, and sampling bias can significantly alter genetic variability within populations. The findings suggest that the east coast's genetic diversity is likely underestimated and that more comprehensive data, including high-throughput genomic analyses and ecological studies, are needed to determine the native range of <em>H. dianthus</em> conclusively. This study underscores the complexity of using genetic data to trace the biogeography and invasion pathways of marine species.</p>
TGIRT-seq of Inflammatory Breast Cancer Tumor and Blood Samples Reveals Widespread Enhanced Transcription Impacting RNA Splicing and Intronic RNAs in Plasma
<p>Supplemental file containing results of mapping statistics, DESeq2 analysis, peak calling analysis, and IDR analysis.</p>
Decoding Gut-Brain Biomarkers and Developing a Minimally Intrusive Gut Microbiome Sampling: Enhancing Cognitive Well-being in Athletes
ClinicalTrials.gov study NCT07093112. IPD Sharing: NO. Countries: 1. Publications: 0.
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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.