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464 results for “model structure”
Evaluation of Mask R-CNN Model for Counting Reproductive Structures of Six Plant Species 1895-2018
Phenology––the timing of life-history events––is a key trait for understanding responses of organisms to climate. The digitization and online mobilization of herbarium specimens is rapidly advancing our understanding of plant phenological response to climate and climatic change. The current common practice of manually harvesting data from individual specimens greatly restricts our ability to scale data collection to entire collections. Recent investigations have demonstrated that machine-learning models can facilitate data collection from herbarium specimens. However, present attempts have focused largely on simplistic binary coding of reproductive phenology (e.g., flowering or not). Here, we use crowd-sourced phenological data of numbers of buds, flowers, and fruits of more than 3000 specimens of six common wildflower species of the eastern United States (Anemone canadensis, A. hepatica, A. quinquefolia, Trillium erectum, T. grandiflorum, and T. undulatum} to train a model using Mask R-CNN to segment and count phenological features. A single global model was able to automate the binary coding of reproductive stage with greater than 90% accuracy. Segmenting and counting features were also successful, but accuracy varied with phenological stage and taxon. Counting buds was significantly more accurate than flowers or fruits. Moreover, botanical experts provided more reliable data than either crowd-sourcers or our Mask R-CNN model, highlighting the importance of high-quality human training data. Finally, we also demonstrated the transferability of our model to automated phenophase detection and counting of the three Trillium species, which have large and conspicuously-shaped reproductive organs. These results highlight the promise of our two-phase crowd-sourcing and machine-learning pipeline to segment and count reproductive features of herbarium specimens, providing high-quality data with which to study responses of plants to ongoing climatic change.
Non-perturbative phase structure of the bosonic BMN matrix model --- data release
<p>This HDF5 file collects data and analysis results for non-perturbative lattice calculations investigating the phase structure of the bosonic part of the Berenstein--Maldacena--Nastase matrix model. See the README for further information.</p>
GFN2-xTB structures of iCOM adsorbed on a cluster model of water molecules derived from a periodic model of crystalline ice
<p>This dataset contains the atomic coordinates in the <a href="http://www.moldraw.unito.it/">.</a>xyz format of the GFN2-xTB optimized structures of 20 iCOMs adsorbed at the surface of a cluster of 84 water molecules mimicking the periodic model of crystalline water icy grain as described by Ferrero, S.; Zamirri, L., Ceccarelli, C.; Witzel, A.; Rimola, A.; Ugliengo, P. ApJ, (2020) 904:11. For all considered structures we also provided a specific file in the Gaussian format with the computed harmonic frequencies. Each file can be easily converted in input for the variety of quantum mechanical programs, like VASP, QE, Gaussian 16 etc.</p> <p> </p> <p> </p>
Unveiling the atomistic and electronic structure of NiII–NO adduct in a MOF-based catalyst by EPR spectroscopy and quantum chemical modelling
<p><strong>Description of the dataset: </strong></p> <ul> <li><strong>Data type</strong>: Experimental spectroscopic measurements, computer simulation and analysis</li> <li>Files are with filename extensions: <strong>DSC</strong>, <strong>DAT</strong>, <strong>m</strong>, <strong>txt</strong></li> <li>Information on <strong>origin of the data</strong>:</li> </ul> <ul> <li>EPR spectroscopic measurements with filename extensions <strong>DSC</strong>, <strong>DTA.</strong></li> <li>EPR spectroscopic simulation and analyses with filename extension <strong>m</strong>.</li> <li>EPR spectra are exported as <strong>txt</strong> files in ASCII format.</li> </ul> <ul> <li>X-band CW-EPR spectroscopic measurements were generated by EMX spectrometer equipped with SHQ cavity produced by Bruker.</li> <li><strong>If the dataset includes multiple files that relate to each other:</strong> <ul> <li>Files in <strong>PARACAT_WP4_20230706_01_CW_Xband </strong>folder includes X-band CW-EPR spectroscopic measurements; original data are in DTA/DSC and txt formats.</li> <li>Files in <strong>PARACAT_WP4_20230706_02_HYSCORE </strong>and <strong>PARACAT_WP4_20230706_03_ENDOR </strong>folders include X-band HYSCORE and ENDOR data; original data are in DTA/DSC and txt formats.</li> <li>Files in <strong>PARACAT_WP4_20230706_ 04_MATLAB</strong> and<strong> PARACAT_WP4_20230706_ 05_Modelling</strong> folders include matlab and computer simulations/analyses of the EPR measurements; data are in m and txt formats.</li> <li>File <strong>PARACAT_WP4_20230706_ 06_Origin</strong> include origin plotted data</li> </ul> </li> </ul> <p> </p> <ul> <li><strong>Information on</strong>: <ul> <li>specialized abbreviations: <strong>MFU– </strong>MFU-4l:NO<sub>2</sub> MOF material</li> <li>NiNO – NO adsorbed MFU-4l:NO<sub>2</sub> MOF</li> <li>@10K – measured at 10 K</li> <li>definitions of variables: <strong>Magnetic field, Temperature.</strong></li> <li>units of measurement: <strong>Gauss (G), K, degree (°), milliTesla (mT)</strong>.</li> </ul> </li> </ul>
Genome-wide structure and function modeling of SARS-COV-2
<p>Homology models and function annotation for all proteins in the SARS-CoV-2 genome. For a description of each file, follow <a href="https://zhanglab.ccmb.med.umich.edu/COVID-19/">this link</a>. </p>
UM experiments for "Continuous Structural Parameterization: A proposed method for representing different model parameterizations within one structure demonstrated for atmospheric convection"
<p>NetCDF4 files containing UM vn 11.1 data used in Lambert et al., 2020, Continuous Structural Parameterization: A proposed method for representing different model parameterizations within one structure demonstrated for atmospheric convection, submitted to Journal of Advances in Modeling Earth Systems.</p> <p>Key:</p> <p>"summaryday.nc" contain eleven months of data in each year, excluding either February or March.</p> <p>"summarydat2.nc" contain one month of data in each year, either February or March.</p> <p>"last5" indicates that for this simulation only the last five years of data are available.</p> <p>"llcs" are simulations with Lambert-Lewis.</p> <p>"gr" are simulations with Gregory-Rowntree.</p> <p>"llcsemu" are simulations with the Lambert-Lewis emulator.</p> <p>"gremu" are simulations with the Gregory-Rowntree emulator.</p> <p>"llcsemu_llcs" is the test simulation wherein the LLCS emulator is run equatorward of 30 degrees and the original LLCS convection scheme is run poleward of 30 degrees.</p> <p>"4xco2" have 4 x pre-industrial atmospheric carbon dioxide concentration. (Others have 1 x pre-industrial atmospheric carbon dioxide concentration.)</p> <p>"rh0.7" and "rh0.9" have LLCS RHCRIT set to 70% and 90% respectively.</p> <p>"30day" are one month simulations for July for which daily output are available. Other data are monthly mean only.</p> <p> </p>
Radiative transfer modeling in structurally-complex stands: what aspects matter most?: Dataset
<p>This repository is linked to the paper "Radiative transfer modeling in structurally-complex stands: what aspects matter most?" submitted to Annals of Forest Science and written by Frédéric ANDRÉ (corresponding author), Louis DE WERGIFOSSE, François DE COLIGNY, Nicolas BEUDEZ, Gauthier LIGOT, Vincent GAUTHRAY-GUYÉNET, Benoit COURBAUD and Mathieu JONARD.</p> <p>The repository contains the three following files :</p> <ul> <li>CalibrationResults.csv: Bayes factors and summary statistics of parameter estimates for each calibration run</li> <li>ParameterPosteriorDistributions.csv: median values and 90% credible intervals for the parameter posterior distributions</li> <li>StatisticalComparison.csv: statistics (Fractional bias, Root mean square error, Paired Student test, Pearson correlation coefficient, Parameters of the Deming regression between observed and predicted values) used to compare the 'Best model configurations'</li> </ul> <p>For more information concerning this repository or the study, please do not hesitate to contact Frédéric ANDRÉ (frederic.andre@uclouvain.be) or Mathieu JONARD (mathieu.jonard@uclouvain.be).</p>
Datasets of sequences, alignments and structural models generated for the structural prediction of complexes mediated by intrinsically disordered regions.
<p>This repository contains input and ouput files used and generated for the scanning of intrinsically disordered region and the prediction of their binding sites to receptor proteins using the <a href="https://github.com/i2bc/SCAN_IDR">SCAN_IDR</a> pipeline with AlphaFold2-Multimer.</p><p>It contains two archives: </p><ol><li><a href="https://zenodo.org/api/records/10068949/draft/files/scanidr_data_repository_corr6J08.tar/content"><i><strong>scanidr_data_repository_corr6J08.tar</strong></i></a> dedicated to the analysis of a dataset of 42 protein complexes non redundant with the dataset used for AlphaFold2 training,</li><li><a href="https://zenodo.org/api/records/10068949/draft/files/923_elm_cases_repository.tar.gz/content"><i><strong>923_elm_cases_repository.tar.gz</strong></i></a> dedicated to the analysis of 923 complexes from the ELM database.</li></ol><p>These data can be used to rerun specific sections of the pipeline and scripts provided in: <a href="https://github.com/i2bc/SCAN_IDR">https://github.com/i2bc/SCAN_IDR</a></p><h4><strong>Dataset of 42 non redundant complexes</strong></h4><p>The first archive <a href="https://zenodo.org/api/records/10068949/draft/files/scanidr_data_repository_corr6J08.tar/content"><i><strong>scanidr_data_repository_corr6J08.tar</strong></i></a> contains 3 compressed directories and a README file detailing their contents :</p><ul><li>the initial raw sequence and alignment data for every chain -> DIRECTORY <strong>fasta_msa/</strong></li><li>the input and output data of every Alphafold run for every complex -> DIRECTORY <strong>af2_runs/</strong></li><li>the native reference structures -> DIRECTORY <strong>ref_capri_curated/</strong></li></ul><p>The protein-peptide complex cases have been assigned a distinct index number, from 1 to 42, consistent across the several directories of the archive. Their corresponding directories are labelled as <i><index>_<pdbcode></i>.</p><p><i>The models in this archive were generated using AlphaFold2-Multimer v2.2</i></p><h4><strong>Dataset of 923 complexes selected from the ELM database</strong></h4><p>The second archive <a href="https://zenodo.org/api/records/10068949/draft/files/923_elm_cases_repository.tar.gz/content"><i><strong>923_elm_cases_repository.tar.gz</strong></i></a> contains input and ouput files used and generated for the analysis of 923 Eukaryotic Linear Motifs (ELM) database entries.</p><p>Each ELM entry is indexed with specific integer id and is composed of a receptor and a ligand protein. </p><p>The archive contains a Table associating ELM indexes with the ELM entry information, 5 directories and a README file detailing their contents:</p><ul><li>the table describing ELM entries -> FILE <strong>Table_923ELM_uid_delimitations_info_for_archive.txt</strong></li><li>the initial raw sequence and multiple sequence alignment (MSA) data for every chain -> DIRECTORY <strong>fasta_msa/</strong></li><li>the concatenated MSA model for every ELM complex and protocol used -> DIRECTORY <strong>af2_elm_coali_inputs/</strong></li><li>the best model of every AF2 protocol for every complex according to the AF2 -> DIRECTORY <strong>af2_elm_models/</strong></li><li>the best model cut in the ligand part to select only the ELM motifs as used for the evaluation of the models -> DIRECTORY <strong>elm_cut_models/</strong></li><li>the reference structures used for the evaluation of the models -> DIRECTORY <strong>ref_capri_curated/</strong></li></ul><p><i>The models in this archive were generated using AlphaFold2-Multimer v2.3</i></p>
Mangrove terrestrial laser scanning (TLS) point clouds and quantitative structural models (QSMs)
<p>Datasets for a publication entitled, "Terrestrial laser scanning for the estimation of above ground biomass of mangrove roots by modelling them as inverted trees."</p> <p>See the file "Data dictionary for Mangrove terrestrial laser scanning.pdf" for a description of the datasets included in the zipped folder. </p>
Compiled database, code and raw data for the article "A Comprehensive Database of Leaf Temperature, Water, and CO2 Fluxes in Young Oil Palm Plants Across Diverse Climate Scenarios for the Evaluation of Functional-Structural Models"
<p>This dataset results from an experiment on young oil palm plants (<em>Elaeis guineensis</em>) in the Ecotron facility from CNRS in Montpellier. Four plants were put in a microcosm one by one with varying climatic conditions to investigate the effect of climate on leaf temperature, CO2, and H2O fluxes at the plant scale. The conditions were defined based on typical daily conditions from a location where it is grown (Libo, Indonesia), <em>i.e.</em>, a day with no rainfall and near-average air temperature and humidity. This base condition was then modified by adding more CO2 (400, 600 and 800ppm), less radiation (typical cloudy sky), and more or less temperature and vapour pressure deficit (± 30%).</p> <p>Find more details from the <code>README.md</code> file in the repository or from the associated <a href="https://github.com/PalmStudio/Biophysics_database_palm" target="_blank" rel="noopener">Github repository</a>.</p>
Data supporting the publication "Many-body quantum sign structures as non-glassy Ising models"
<p>This repository contains all raw data that were used to draw conclusions and generate figures for the paper:</p> <p><strong>"Many-body quantum sign structures as non-glassy Ising models"</strong><br> by Westerhout, T., Katsnelson, M. I., & Bagrov, A. A.</p> <p><em>Abstract:</em> The non-trivial phase structure of the eigenstates of many-body quantum systems severely limits the applicability of quantum Monte Carlo, variational, and machine learning methods. Here, we study real-valued signful ground-state wave functions of frustrated quantum spin systems and, assuming that the tasks of finding wave function amplitudes and signs can be separated, show that the signs can be easily bootstrapped from the amplitudes. We map the problem of finding the sign structure to an auxiliary classical Ising model defined on a subset of the Hilbert space basis. We show that the Ising model does not exhibit significant frustrations even for highly frustrated parental quantum systems, and is solvable with a fully deterministic O(K log K)-time combinatorial algorithm (where K is the Ising model size). Given the ground state amplitudes, we reconstruct the signs of the ground states of several frustrated quantum models, thereby revealing the hidden simplicity of many-body sign structures.</p>
A 3-D model of The Bear Trap: A unique stone structure on the northwest tip of the Nuussuaq Peninsula, Greenland
<p>This dataset consists of five files. The .obj, .jpg., and .mtl files can be used to view a high-resolution 3D mesh model of ‘The Bear Trap’, a unique Norse ruin at the western end of the Nuussuaq Peninsula in NW Greenland (also called ‘Bjørnefælden’ in Danish, and ‘Putdlagssuaq’ or ‘The Great Trap’ Greenlandic Kalaallisut). The .laz file contains the dense cloud. The .avi shows a flyover video of the 3D model. The 3D model was created from 1686 photographs that were processed using Structure from Motion Multiview Stereo photogrammetry software (in this case Agisoft Metashape Pro v1.7; Linux Ubuntu). A 24.3 megapixel Sony a5100 APS-C mirrorless camera fitted with a 24 mm lens was used to acquire ground-level imagery of the structure. The image alignment or bundle adjustment was performed using ‘High’ accuracy, a key point limit of 60000 and no tie point limit. The sparse point cloud was scaled using three markers with known dimensions that were placed in the area of interest, and which remained stationary throughout the entire photo survey. The dense point cloud was computed using the ‘High’ setting. The dense point cloud was then used to compute the mesh model using the ‘High’ setting. Instructions are provided in the readme file that accompanies this dataset. </p> <p>The image survey of the Bear Trap was conducted as part of the Vaigat Iceberg-Microbial Oil Degradation and Archaeological Heritage Investigation (VIMOA) project, which was funded by the Danish Centre for Marine Research and supported by the Arctic Research Centre at Aarhus University, the National Museum of Denmark, the Greenland Institute of Natural Resources, and The Greenland National Museum and Archives in Nuuk. Permits for the survey were obtained in advance from the Greenland National Museum and Archives in Nuuk. Walsh et al. (2020) provides an overview of the archaeological surveys conducted during the VIMOA project and Walsh et al. (submitted) provides further details specific to The Bear Trap and surrounding archaeological contexts. </p> <p>Walsh et al. (2020) The VIMOA project and archaeological heritage in the Nuussuaq Peninsula of north-west Greenland. <em>Antiquity</em> 94:e6 doi:10.15184/aqy.2019.230</p> <p>Walsh, Matthew J., Daniel F. Carlson, Pelle Tejsner, and Steffen Thomsen. The Bear Trap: Reinvestigating a unique stone structure on the northwest tip of the Nuussuaq Peninsula, Greenland. Manuscript submitted to <em>Arctic Anthropology</em></p>
Effect of MgO sintering additive on mullite structures manufactured by fused deposition modeling (FDM) technology
<p>An optimized recipe for 3D printing of Mullite-based structures was used to investigate the effect of MgO sintering additive on the processing stages and final ceramic properties. To achieve dense 3:2 mullite, ceramic filaments were prepared based on an alumina powder, a methyl silicone resin, EVA elastomeric binder and MgO powder. Using 1 wt% MgO and a dwell time of 5 h at 1600 °C, a dense mullite structure could be obtained from filaments with a diameter of 1.75 mm. Ceramic structures with and without sintering additive were printed in vertical and horizontal direction, to investigate the effect of printing direction on mechanical strength after sintering. Using four-point bending test, it was demonstrated that by using MgO, the printing orientation did not affect the mechanical strength significantly anymore. The low Weibull modulus could be explained by the closed porosity that emerge during the degassing of the preceramic polymer due to cross-linking.</p>
Data, plotting scripts, and figures for "Assessing diffusion model impacts on enstrophy and flame structure in lean premixed flames"
<p>This repository contains the data, plotting scripts, and figures associated with the paper "Assessing diffusion model impacts on enstrophy and flame structure in lean premixed flames" by Aaron J. Fillo, Peter E. Hamlington, and Kyle E. Niemeyer.</p> <p>See the README file for additional details.</p>
Experimental Seismic Data Obtained Using a 3D-Printed Model of the Los Angeles Basin Structure
<p>These data were obtained and analyzed by Park et al., (2022) "Seismic wave simulation using a 3D printed model of the Los Angeles Basin" (doi:10.1038/s41598-022-08732-w).</p> <p> </p>
Data to publication: Fibre optic measurements and model uncertainty quantification for Fe-SMA strengthened concrete structures
<p>This dataset contains the results of an experimental campaign, presented in the publication "Fibre optic measurements and model uncertainty quantification for Fe-SMA strengthened concrete structures". The publication covers fibre optic measurements inside large-scale specimens subjected to external load. The specimens comprised reinforced concrete slabs, strengthened with reinforcement bars made from iron-based shape memory alloy.</p>
An Integrated Structural Model of the DNA Damage Responsive H3K4me3 Binding WDR76:SPIN1 Complex with the Nucleosome
<p>Serial Capture Affinity Purification (SCAP) is a powerful method to isolate a specific protein complex. When combined with cross linking mass spectrometry (XL-MS) and computational approaches one can build an integrated structural model of the isolated complex. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone marker reader that specifically recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to a previous SCAP analysis of the SPIN1:SPINDOC complex, histones and the H3K4me3 mark were copurified with the WDR76:SPIN1 complex. Next, interaction network analysis of copurifying proteins and microscopy analysis revealed a potential role of the WDR76:SPIN1 complex in the DNA damage response. Since we detected an extensive number of cross-linked sites were found between WDR76, SPIN1, and histones, we first built an integrated structural model of the complex which revealed that SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Finally, we then used the powerful Integrative Modeling Platform to build a structural model of WDR76 and SPIN1 bound to the nucleosome.</p>
Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling
<p>The slow but spontaneous and ubiquitous formation of C3(H2O), the hydrolytic and conformationally rearranged product of C3, initiates antibody-independent activation of the complement system that is a key first line of antimicrobial defense. The structure of C3(H2O) has not been determined. Here we subjected C3(H2O) to quantitative cross-linking/mass spectrometry (QCLMS). This revealed details of the structural differences and similarities between C3(H2O) and C3, as well as between C3(H2O) and its pivotal proteolytic cleavage product, C3b, which shares functionally similarity with C3(H2O). Considered in combination with the crystal structures of C3 and C3b, the QCMLS data suggest that C3(H2O) generation is accompanied by the migration of the thioester-containing domain of C3 from one end of the molecule to the other. This creates a stable C3b-like platform able to bind the zymogen, factor B, or the regulator, factor H. Integration of available crystallographic and QCLMS data allowed the determination of a 3D model of the C3(H2O) domain architecture. The unique arrangement of domains thus observed in C3(H2O), which retains the anaphylatoxin domain (that is excised when C3 is enzymatically activated to C3b), can be used to rationalize observed differences between C3(H2O) and C3b in terms of complement activation and regulation.</p> <p><strong>For more information</strong> about how to reproduce this modeling, see the <a href="https://salilab.org/Complement/">Sali lab website</a> or the README file.</p>
Data for "SeaMoon: from protein language models to continuous structural heterogeneity"
<p>Datasets used for development of SeaMoon: <br><a href="https://github.com/PhyloSofS-Team/seamoon">https://github.com/PhyloSofS-Team/seamoon</a>.</p> <p>This upload contains the following data:</p> <ul> <li><strong>precomputed_emb.tar.gz</strong> is a compressed archive containing the precomputed data used for training and testing the models of the SeaMoon method, in Torch <strong>.pt </strong>format. <br>The file prefixes consist of two IDs, "ID1_ID2_", identifying the <a href="https://github.com/PhyloSofS-Team/DANCE">DANCE</a> [1] protein conformational collection used for its generation. "ID1" represents the first member of the collection in alphabetical order, while "ID2" is the reference conformation for the structural alignment. The "ESM_data" or "ProstT5_data" suffixes designate the type of embeddings, generated by either ESM2 [2] or ProstT5 [3].<br>The dictionnary contains the following keys: <ul> <li><strong>emb:</strong> The per-residue embedding.</li> <li><strong>data: </strong>A tuple containing "ID2" (the reference), the amino acid sequence, and the coverage of the positions in the original DANCE collection.</li> <li><strong>eigvect:</strong> The eigenvectors of the covariance matrix of the "ID1_ID2" collection, centered on reference conformaton "D2".</li> <li><strong>eigval: </strong>The associated eigenvalues.</li> <li><strong>ref:</strong> The coordinates of the C-alpha atoms of the reference conformaton "ID2".</li> </ul> </li> <li><strong>train_list.txt, train_list_5ref.txt, val_list.txt </strong>and<strong> test_list.txt</strong> contain the identifiers of the samples used for training and evaluating the SeaMoon models. In the "5ref" setting, we used up to 5 reference conformations per collection. </li> </ul> <p>For details on SeaMoon see:</p> <div> <div>SeaMoon: Prediction of molecular motions based on language models</div> </div> <div>Valentin Lombard, Dan Timsit, Sergei Grudinin, Elodie Laine</div> <div>bioRxiv 2024.09.23.614585; doi: https://doi.org/10.1101/2024.09.23.614585</div> <div> </div> <div>For more information on data usage and generation please see <a href="https://github.com/PhyloSofS-Team/seamoon">https://github.com/PhyloSofS-Team/seamoon</a>.</div> <div> </div> <div>Abstract:</div> <p>How protein move and deform determines their interactions with the environment and is thus of utmost importance for cellular functioning. Following the revolution in single protein 3D structure prediction, researchers have focused on repurposing or developing deep learning models for sampling alternative protein conformations. In this work, we explored whether continuous compact representations of protein motions could be predicted directly from protein sequences, without exploiting nor sampling protein structures. Our approach, called SeaMoon, leverages protein Language Model (pLM) embeddings as input to a lightweight (~1M trainable parameters) convolutional neural network. SeaMoon achieves a success rate of up to 40% when assessed against ~1,000 collections of experimental conformations exhibiting a wide range of motions. SeaMoon capture motions not accessible to the normal mode analysis, an unsupervised physics-based method relying solely on a protein structure's 3D geometry, and generalises to proteins that do not have any detectable sequence similarity to the training set. SeaMoon is easily retrainable with novel or updated pLMs. </p> <p> </p> <p>[1] Lombard, V.; Grudinin, S.; Laine, E. Explaining Conformational Diversity in Protein Families through Molecular Motions. Scientific Data 2024, 11, 752.</p> <p>[2] Lin, Z.; Akin, H.; Rao, R.; Hie, B.; Zhu, Z.; Lu, W.; Smetanin, N.; Verkuil, R.; Kabeli, O.; Shmueli, Y.; Dos Santos Costa, A.; Fazel-Zarandi, M.; Sercu, T.; Candido, S.; Rives, A. Evolutionary-scale prediction of atomic-level protein structure with a language model. Science 2023, 379, 1123–1130.</p> <p>[3] Heinzinger, M.; Weissenow, K.; Sanchez, J. G.; Henkel, A.; Steinegger, M.; Rost, B. ProstT5: Bilingual language model for protein sequence and structure. bioRxiv 2023, 2023–07.</p>
Computed surface and chemical potentials, expansion coefficients, structures, models and results for the PMFPredictor Toolkit
<p>The PMFPredictor toolkit enables the prediction of the potentials of mean force describing the interaction between a surface and a small molecule in aqueous solution, which would otherwise be obtained from lengthy metadynamics simulations. This repository contains files to enable the operation of the toolkit, with source code available at https://github.com/ijrouse/PMFPredictor-Toolkit and corresponding to release v0.5-alpha.</p> <p>In PMFPredictor-Repository.zip we provide supplementary data necessary for the operation of the PMFPredictor Toolkit including:</p> <ul> <li>Structures of surfaces ("Structures/Surfaces") and chemicals ("Structures/Chemicals") in a united tabulated (.csv) format, listing x/y/z co-ordinates, atom IDs, mass (in amu), charge (in elementary units), Lennard Jones 6-12 parameters: sigma (in nm) and epsilon (in kJ/mol).</li> <li>Interaction potentials of surfaces ("SurfacePotentials") and chemicals ("ChemicalPotentials") with probe atoms and molecules in tabulated format with distances relative to reference points in nm and energies in kJ/mol. Also included in these folders are the potentials with the molecular probes in individual files.</li> <li>Hypergeometric expansion coefficients of the interaction potentials ("Datasets/SurfacePotentialCoefficientsNoise-1-oct12.csv" and "Datasets/ChemicalPotentialCoefficients-oct10.csv") in tabulated form, corresponding to potentials with units of nm for distance and kJ/mol for energy. Descriptions of the headers are provided in DatasetHeaderDescription.txt, included in the archive.</li> <li>Trained TensorFlow models for the prediction of potentials of mean force from HG interaction coefficients, suitable for loading via the Keras backend.</li> <li>PMFs generated for a range of surfaces and chemicals as output from the trained model, in both text format and figures showing comparisons to training PMFs where available. PMFs are supplied as tabulated data with comma separated values of distance in nm and interaction energies in kJ/mol.</li> <li>Adsorption energies in kJ/mol evaluated at T=300K extracted from all PMFs and compared to the values obtained from known PMFs where available.</li> </ul> <p>The surface_pmfpredictor.zip archive contains PMFs selected for the operation of the UnitedAtom software package for the calculation of protein-nanoparticle interactions. This data is included in the main repository file and provided separately to avoid the download of unnecessary data if only the final PMFs are required. As with the main set, these are provided in tabulated form with distance [nm], energy [kJ/mol] pairs. This repository also contains the sets of figures illustrating these PMFs for each surface. Both archives contain further information on the contents, including descriptions of the surfaces and chemicals for which PMFs are computed. We also supply the training data used to build the model in a separate archive, PMFPredictor-TrainingData.zip, along with a text file containing descriptions of all headers in this file. This training data is quite large when uncompressed, c.a. 7 Gb, hence its exclusion from the main archive.</p> <p>If you use results from this repository please cite the following paper in addition to the repository itself:</p> <p>I. Rouse, V. Lobaskin, Machine-learning based prediction of small molecule -- surface interaction potentials, arXiv:2211.07999<br> https://arxiv.org/abs/2211.07999</p>
ScienceDex guides
Understand access before you commit
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.