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3,988 results for “Rosetta”
METL Rosetta datasets
<p>This repository contains the biophysical attributes used to pretrain METL-Local and METL-Global models. We provide raw Rosetta data as well as processed Rosetta datasets that have duplicates, outliers, and NaN values removed.</p> <p>Users of these datasets should cite both <a href="https://doi.org/10.1038/s41592-025-02776-2">METL</a> and <a href="https://github.com/RosettaCommons/rosetta/blob/main/CITING_ROSETTA.md">Rosetta</a>.</p> <p>The repository also contains packaged conda environment files needed to generate new Rosetta simulation data in the OSPool with our <a href="https://github.com/gitter-lab/metl-sim/tree/master/notebooks/osg">Jupyter notebook</a>.</p> <div> <h2>Raw Rosetta data</h2> <p>Raw Rosetta data comes in the form of SQLite databases in the .db format. There are separate databases for each of the local datasets as well as the global dataset. Note the GB1-IgG binding raw data only contains the binding scores, whereas the processed GB1-IgG binding dataset listed below contains both the binding and standard scores. The processed dataset was created by combining the raw GB1-IgG binding data with the raw GB1 standard data.</p> <div> <h2>Processed Rosetta datasets</h2> </div> <div> <p>Each processed Rosetta dataset has its own directory containing the following:</p> <ul> <li>The dataset in three formats (.tsv, .db, and .h5 files), all containing the same data</li> <li>A list of PDB files corresponding to the variants in the dataset (pdb_fns.txt)</li> <li>A splits directory containing train, validation, and test splits we used for pretraining</li> <li>Standardization parameters computed on the train set (in the splits directory)</li> </ul> <p>Processed Rosetta datasets can be used directly with the main <a href="https://github.com/gitter-lab/metl">metl</a> GitHub repository to pretrain models. That repository also contains a small <a href="https://github.com/gitter-lab/metl/tree/main/data/rosetta_data">example dataset</a>.</p> <p>Our <a href="https://github.com/gitter-lab/metl-pub/tree/main/data/rosetta_data">metl-pub</a> GitHub repository has a mapping from the dataset names to these filenames and instructions for reading the files.</p> <h2>conda environment files</h2> <p>clean_pdb_2025-02-13.tar.gz and metl-sim_2025-02-13.tar.gz are packaged conda environment files from the <a href="https://github.com/gitter-lab/metl-sim">metl-sim</a> GitHub repository.</p> </div> </div>
Structural modeling of hERG channel: Drug interactions using Rosetta
<p>Human Ether-a-go-go-Related Gene (hERG) encodes a potassium-selective voltage-gated ion channel essential for normal electrical activity in the heart but is also a major drug anti-target. Genetic hERG mutations and blockage of the channel pore by drugs can cause long QT syndrome (LQTS), which predisposes individuals to potentially deadly arrhythmias. However, not all hERG blocking drugs are pro-arrhythmic, and their differential affinities to discrete channel conformational states have been suggested to contribute to arrhythmogenicity. We used Rosetta electron density refinement and homology modeling to build structural models of open-state hERG channel wild-type (WT) and mutant variants (Y652A, F656A, and Y652A/F656A), and a closed state WT channel based on cryo-electron microscopy structures of hERG and EAG1 channels. These models were used as protein targets for molecular docking of charged and neutral forms of amiodarone, nifekalant, dofetilide, d/l-sotalol, flecainide, and moxifloxacin. We selected these drugs based on their different arrhythmogenic potentials and abilities to facilitate hERG current. Our docking studies and clustering provided atomistic structural insights into state-dependent drug–channel interactions l that play a key role in differentiating safe and harmful hERG blockers and can explain hERG channel facilitation through drug interactions with its open-state hydrophobic pockets.</p>
Accurate Prediction of Enzyme Thermostabilization with Rosetta using AlphaFold Ensembles
<p>DT<sub>M</sub> vs DG<sub>f,mut</sub> values for scoring LovD, LipA, <em>p</em>-nitrobenzyl esterase, xylanase A and tryptophan 6-halogenase variants (<em>DTM_vs_DDGf_mut.xlsx</em>).</p> <p>AlphaFold predicted structures in PDB and Pymol sessions formats for top scoring LovD, LovD6, LovD9, LipA WT, LipA 6B, <em>p</em>-nitrobenzyl esterase WT, xylanase A WT and tryptophan 6-halogenase WT decoys (<em>mAF-min_ensembles.zip</em>).</p> <p>Rosetta energies for all calculations (<em>Rosetta_scores.zip</em>).</p>
Structural modeling of hERG channel: Drug interactions using Rosetta
Open the record for dataset details and reuse information.
Dataset for Waves during Rosetta's close flyby of comet 67P
<p>All data used in the article Ion acoustic waves near a comet nucleus: Rosetta observations at comet 67P/Churyumov-Gerasimenko by Herbert Gunell, Charlotte Goetz, Elias Odelstad, Arnaud Beth, Maria Hamrin, Pierre Henri, Fredrik L. Johansson, Hans Nilsson, and Gabriella Stenberg Wieser ( Annales Geophysicae, vol. 39, 53–68, 2021, doi: 10.5194/angeo-39-53-2021 ) can be found in this package together with the matlab m-files that were used to produce the figures in that article.</p> <p> </p>
'Psyché' as a Rosetta stone? Assessing collaborative authorship in the French 17th century theatre -- supplementary material
<p>Supplementary material for the paper:</p> <p>‘Psyché’ as a Rosetta Stone? Assessing Collaborative Authorship in the French 17th Century Theatre</p> <p>presented at Computational Humanities Research 2021.</p>
Refractory Overactive Bladder: Sacral NEuromodulation v. BoTulinum Toxin Assessment (ROSETTA)
ClinicalTrials.gov study NCT01502956. IPD Sharing: NO. Countries: 1. Publications: 5.
Models, Data, and Scripts Underlying "Robustification of RosettaAntibody and Rosetta SnugDock"
<p>This repository contains the models, data, and scripts underlying the publication "Robustification of RosettaAntibody and Rosetta SnugDock" by <a href="https://www.biorxiv.org/content/10.1101/2020.05.26.116210v1.abstract">Jeliazkov et al.</a> Brief descriptions of the individual compressed files follow.</p> <ul> <li>fkic_H3.zip/master_H3.zip contain the models underlying Figure 4A. The models are compared against their corresponding crystal structures and the backbone RMSD is calculated for the CDR H3 (residues 95-102, Chothia definition). Each zip file contains PDB-labeled directories with homology models in the base directory and loop models in the "models" subdirectory. The "master" zip used the standard H3 modeling approach in RosettaAntibody. The "fkic" directory used the standard method plus fragment insertion.</li> <li>fragment_comparison.zip contains the scripts and raw data for Figure 4B.</li> <li>fragments.tar.gz contains the fragments used to model the antibodies loops (Figure 4A) and for the comparison in Figure 4B. The traditional protein loop models and fragments in Figure 4B are published separately by <em>Pan et al.</em> [to do: update citation].</li> <li>grafting_results.zip contains the data and analysis code behind Figure 3.</li> <li>other_stray_code.zip contains the analysis code for Figures 1, 5, and the supplemental figures.</li> <li>snugdock_example.zip contains the raw data for Figure 5 which is also to be published separately by <em>Zhou et al.</em> [to do: update citation].</li> </ul>
FIGURE 124 in A Rosetta Stone for eastern Pacific Caecidae (Gastropoda: Caenogastropoda)
FIGURE 124. Caecum sp. B. A. Profile view with periostracum (LACM 1962-22.33). B. Profile view without periostracum (LACM 1962-22.33). C. Profile view (LACM 1962-22.33). D. Ventral view (LACM 1962-22.33). E. Close-up of surface (LACM 1962-22.33).
FIGURE 128. A. C in A Rosetta Stone for eastern Pacific Caecidae (Gastropoda: Caenogastropoda)
FIGURE 128. A. C. venustum (SBMNH 619832). B. C. galapagoense (LACM 3755). C. C. semicinctum (LACM 1972-63.90). D. C. cocoense (SBMNH 619898). E. C. shaskyi (SBMNH 637733). F. C. lucidum (SBMNH 452540). G. C. sp. A (LACM 1972-52.67). H. C. sp. B (LACM 1962-22.33). I. C. sp. C (BCD collection, NHMLAC).
FIGURE 123 in A Rosetta Stone for eastern Pacific Caecidae (Gastropoda: Caenogastropoda)
FIGURE 123. Caecum sp. A. A. Profile view with periostracum (LACM 1972-52.67). B. Profile view without periostracum (LACM 1972-52.67). C. Profile view (LACM 1972-52.67). D. Close-up of surface (LACM 1972-52.67). E. Operculum, exterior surface (LACM 1972-52.67). F. C. gulosum holotype, AMS C5919.
FIGURE 120 in A Rosetta Stone for eastern Pacific Caecidae (Gastropoda: Caenogastropoda)
FIGURE 120. Caecum spiculum sp. nov. A. Paratype, profile view with periostracum (SBMNH 637740). B. Paratype, profile view without periostracum (SBMNH 637740). C. Holotype, profile view (SBMNH 637742). D. Paratype, ventral view (SBMNH 637740). E. Paratype, profile view (SBMNH 637740).
FIGURE 115 in A Rosetta Stone for eastern Pacific Caecidae (Gastropoda: Caenogastropoda)
FIGURE 115. Caecum shaskyi sp. nov. shells at different growth stages. A. Teleoconchs III to IV (SBMNH 637733). B. Surface of teleoconch III (SBMNH 637733). C. Teleoconchs IV to VI (SBMNH 637733). D. Surface of teleoconchs IV to VI (SBMNH 637733). E. Teleoconch VI (SBMNH 637733).
FIGURE 127. A. C in A Rosetta Stone for eastern Pacific Caecidae (Gastropoda: Caenogastropoda)
FIGURE 127. A. C. crebricinctum (SBMNH 120619). B. C. superbum (LACM 1965-25.61). C. C. laqueatum (SBMNH 131113). D. C. elongatum (SBMNH 214991). E. C. californicum (LACM 1971-100.31). F. C. subaustrale (LACM 1975- 28.14). G. C. subspirale (LACM 1978-116.17). H. C. mirificum (LACM 1975-54.29). I. C. insculptum (LACM 1972-57.44). J. C. firmatum (LACM 1967-17.44). K. C. quadratum (LACM 1971-98.36). L. C. strangulatum (LACM 1965-21.72). M. C. heptagonum (LACM 1976-7.15). N. C. limnetes (LACM 1968-14.31). O. C. clathratum (LACM 1973-7.45). P. C. diminutum (SBMNH 619893). Q. C. chilense (LACM 1964-16.25).
FIGURE 111 in A Rosetta Stone for eastern Pacific Caecidae (Gastropoda: Caenogastropoda)
FIGURE 111. Caecum draperi sp. nov. A. Holotype, profile view without periostracum (SBMNH 637748). B. Paratype, profile view with periostracum (LACM 3756). C. Paratype, profile view (SBMNH 637747). D. Paratype, profile view (SBMNH 637747). E. Paratype, ventral view (LACM 3756). F. Operculum, profile view (SBMNH 637747). G. Operculum, exterior surface (SBMNH 637747).
FIGURE 107. Caecum adamsi nom. nov. A in A Rosetta Stone for eastern Pacific Caecidae (Gastropoda: Caenogastropoda)
FIGURE 107. Caecum adamsi nom. nov. A. Conceptual reconstruction of growth stages. B. Species distribution map.
FIGURE 109 in A Rosetta Stone for eastern Pacific Caecidae (Gastropoda: Caenogastropoda)
FIGURE 109. Caecum lightfootanum sp. nov. shells at different growth stages. A. Protoconch and teleoconchs I to III (SBMNH 637735). B. Teleoconchs III to IV (SBMNH 637735). C. Surface of teleoconch I (SBMNH 637735). D. Teleoconch V (SBMNH 637735). E. Surface of teleoconchs II to III (SBMNH 637735). F. Surface of teleoconchs IV to VI (SBMNH 637734). G. Teleoconch VI (SBMNH 637734).
FIGURE 108 in A Rosetta Stone for eastern Pacific Caecidae (Gastropoda: Caenogastropoda)
FIGURE 108. Caecum lightfootanum sp. nov. A. Profile view with periostracum (SBMNH 637735). B. Profile view without periostracum (SBMNH 637735). C. Holotype, profile view (SBMNH 637734). D. Paratype, ventral view (SBMNH 637735). E. Paratype, subadult transition, ventral view (SBMNH 637735). F. Operculum, exterior surface (SBMNH 637735).
FIGURE 105. Caecum adamsi nom. nov. A in A Rosetta Stone for eastern Pacific Caecidae (Gastropoda: Caenogastropoda)
FIGURE 105. Caecum adamsi nom. nov. A. Profile view with periostracum (SBMNH 620157). B. Profile view without periostracum (SBMNH 620157). C. Profile view (SBMNH 621392). D. Ventral view (SBMNH 621392). E. Operculum, exterior surface (SBMNH 620157). F. Close-up of apertural rings (SBMNH 621392). G. Elephantanellum carpenteri holotype, USNM 340727.
FIGURE 114 in A Rosetta Stone for eastern Pacific Caecidae (Gastropoda: Caenogastropoda)
FIGURE 114. Caecum shaskyi sp. nov. A. Holotype, profile view with periostracum (SBMNH 637732). B. Paratype, profile view without periostracum (SBMNH 637733). C. Holotype, profile view (SBMNH 637732). D. Paratype, profile view (SBMNH 637733). E. Paratype, ventral view (SBMNH 637733). F. Close-up of periostracum (SBMNH 637733). G. Close-up of surface without periostracum (SBMNH 637733). H. Operculum, exterior surface (SBMNH 637733). I. Operculum, interior surface (SBMNH 637733).
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.