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289 results for “Molecular Structures”
Supplementary material 2 from: Grabowska J, Kvach Yu, Rewicz T, Pupins M, Kutsokon I, Dykyy I, Antal L, Zięba G, Rakauskas V, Trichkova T, Čeirāns A, Grabowski M (2020) First insights into the molecular population structure and origins of the invasive Chinese sleeper, Perccottus glenii, in Europe. NeoBiota 57: 87-107. https://doi.org/10.3897/neobiota.57.48958
Table S2. Values of FST population pairwise.
Molecular ecological network analyses: An effective conservation tool for the assessment of biodiversity, trophic interactions, and community structure
<p>Global biodiversity is threatened by the anthropogenic restructuring of animal communities, which rewires species interaction networks in real-time as individuals are extirpated or introduced. Conservation science and adaptive ecosystem management demands more rapid, quantitative, and non-invasive technologies for robustly capturing changing biodiversity and quantifying species interactions. Here we develop molecular ecological network analyses (MENA) as an ecosystem assessment tool to address these needs. To construct the ecological network, we used environmental DNA from feces to identify the plant and mammal diet of two carnivores: puma (<i>Puma concolor</i>) and bobcat (<i>Lynx rufus</i>); two omnivores: coyote (<i>Canis latrans</i>) and gray fox (<i>Urocyon cinereoargenteus</i>); and two herbivores: black-tailed deer (<i>Odocoileus hemionus</i>) and black-tailed jackrabbit (<i>Lepus californicus)</i> in a well-studied Californian reserve<i>. </i>To evaluate MENA as a comprehensive biodiversity tool, we applied our framework to identify the structure of the network, patterns of trophic interactions, key species, and to assess its utility in capturing the biodiversity of the area. The high dietary taxonomic resolution enabled the assessment of species diversity, niche breadth and overlap. The network analysis revealed a dense ecological network with a high diversity of weakly connected species and a community that is highly modular and non-nested. The significant prevalence of tri-trophic chain and exploitative competition patterns indicates (i) the removal or reintroduction of a top predator would trigger a trophic cascade within this community, directly affecting their prey and indirectly the plant communities, and (ii) the potential impact of indirect effects between two predators that consume the same prey. These results suggest that the recent resurgence of puma in the study area may impact the herbaceous and woody vegetation and the population size of other predators. This effect of fluctuating predator populations and plant communities could be predicted through MENA's fine-scale assessment of the diet selection and the identified keystone species. Although just using a subset of species, MENA more rapidly, accurately, and effectively captured the broader biodiversity of the area in comparison to other methodologies. MENA reconstructed and unveiled the hidden complexity in trophic structure and interaction networks within the community, providing a promising toolkit for biodiversity and ecosystem management.</p>
Predicting Hydrophobicity by Learning Spatiotemporal Features of Interfacial Water Structure: Combining Molecular Dynamics Simulations with Convolutional Neural Networks
<p>Files for reproducing results from Kelkar et al. (JPCB 2020) - Predicting Hydrophobicity by Learning Spatiotemporal Features of Interfacial Water Structure: Combining Molecular Dynamics Simulations with Convolutional Neural Networks</p> <p> </p> <p>This folder contains simulations starter files and also plug-and-play datasets to test ML algorithms on molecular dynamics (MD) simulation data.</p> <p> </p> <p>All analysis scripts can also be found on GitLab on this link: https://gitlab.com/atharva-kelkar/kelkar_et_al_jpcb_2020</p>
The 1.1 Å Structure of the Periplasmic Phosphate-Binding Protein from Stenotrophomonas maltophilia - a crystallisation contaminant identified by molecular replacement using the entire protein database (X-ray diffraction images).
<p>During efforts to crystallise the enzyme 2,4-dihydroxyacetophenone dioxygenase (DAD) from <em>Alcaligenes</em> sp. 4HAP, a small number of strongly diffracting protein crystals were obtained after two years of crystal growth in one condition. The crystals diffracted synchrotron radiation to almost 1.0 Å resolution and were, until recently, assumed to be formed by the DAD protein. However, when another crystal form of this enzyme was eventually solved at lower resolution, molecular replacement using this structure as the search model did not give a convincing solution with the original atomic resolution dataset. Hence we considered that these crystals might be due to a protein impurity, although molecular replacement using the structures of common crystallisation contaminants as search models again failed. A script to perform molecular replacement using MOLREP (Vagin, A. & Teplyakov, A. (2010). Acta Crystallogr. D 66, 22-25.) in which the first chain of every structure in the PDB was used as a search model was run on a multi-core cluster. This identified a number of prokaryotic phosphate binding proteins as scoring highly in the MOLREP peak lists. Calculation of an electron density map at 1.1 Å resolution allowed most of the amino acids to be identified visually and built into the model. A BLAST search then indicated that the molecule was most probably a phosphate binding protein from <em>Stenotrophomonas maltophilia</em> (UniProt ID: B4SL31; gene ID: Smal_2208) and fitting of the corresponding sequence to the atomic resolution map fully corroborated this. Proteins in this family have been linked with the virulence of antibiotic resistant strains of pathogenic bacteria and with biofilm formation. The structure has been refined to an R-factor of 10.15 % and an R-free of 12.46 % at 1.1 Å resolution. The molecule adopts the type-II periplasmic binding protein fold with a number of extensively elaborated loop regions. A fully-dehydrated phosphate anion is bound tightly between the two domains of the protein and interacts with conserved residues and a number of helix dipoles. </p>
A data-and-knowledge driven structure-based molecular generative framework
<p>Dataset for pretraining and finetuning of PocketFlow.</p>
Exploring Conformational Landscapes and Binding Mechanisms of Convergent Evolition for the SARS-CoV-2 Spike Omicron Variant Complexes with the ACE2 Receptor Using AlphaFold2-Based Structural Ensembles and Molecular Dynamics Simulations
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Molecular structures of the antibody-TCR complexes described in the paper by Pitaro et al. in Frontiers in Immunology
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Unveiling the Structural and Functional Implications of Uncharacterized NSPs and Variations in the Molecular Toolkit Across Arteriviruses
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Lumiflavin molecular structures and energies
<p>List of lumiflavin molecular structures in Cartesian coordinates with respective energy, obtained in the work "Molecular Properties and Tautomeric Equilibria of Isolated Flavins".</p>
Original 3D ED datasets of Co DHG and the integrated merged dataset used for structure determination with molecular replacement.
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Comparative structural insights and functional analysis for the distinct unbound states of Human AGO proteins - Molecular dynamics trajectories and analysis scripts
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Data for "Proteome-wide prediction of mode of inheritance and molecular mechanism underlying genetic diseases using structural interactomics"
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Molecular dynamics simulations of BmrA starting from X-ray and cryo-EM structure
<p>This archive contains all the MD trajectories presented in the article<br> 'Drug-bound and -free outward-facing structures of a multidrug ABC exporter point to a swing mechanism'<br> by Chaptal et al,<br> https://doi.org/10.1101/2021.03.12.435132</p> <p><br> MD simulations of the BMRA Xray structure:<br> - 4 replicates with short equilibration:<br> BMRA_Xray_run1<br> BMRA_Xray_run2<br> BMRA_Xray_run3<br> BMRA_Xray_run4 <br> - 2 replicates with long equilibration:<br> BMRA_Xray_run5<br> BMRA_Xray_run6</p> <p>MD simulations of the BMRA Cryo-EM:<br> - 4 replicates with short equilibration:<br> BMRA_Cryo_run1<br> BMRA_Cryo_run2<br> BMRA_Cryo_run3<br> BMRA_Cryo_run4<br> - 2 replicates with long equilibration:<br> BMRA_Cryo_run5<br> BMRA_Cryo_run6</p> <p>MD simulations of BMRA + R6G:<br> BMRA_R6G_run1<br> BMRA_R6G_run2<br> BMRA_R6G_run3</p> <p> </p>
Molecular Dynamics Simulations of HADDOCK-predicted Complex Structures of apoE2 and Factor H
<p>Input and output data for the molecular dynamics simulations of the FH5–7/ApoE2 complex. Initial structures generated with the HADDOCK v2.4 web server with 3 nm distance restraints for lysine pairs that were experimentally found to be cross-linked with DSS. </p> <p>Five clusters and the four representative structures provided by HADDOCK were then used for atomistic molecular dynamics simulations. These structures were solvated and simulated with both CHARMM36m and Amber FF14SB force fields for 250 ns each using GROMACS 2021. The recommended simulation parameters were used for both force fields, and they are available in the mdp files. </p> <p>For each of these 5 (clusters) x 4 (structures per cluster) x 2 (force fields) = 40 simulations, the outputs and inputs are provided; the trajectory (xtc), energy file (edr), final structure (gro), run parameter file (tpr), and continue point (cpt) are system-specific, whereas a single topology (top) and index file (ndx) is shared among all simulations with the same force field. The molecule definitions (itp) referred to in the topology are provided in the compressed files.</p>
Nano-structured Hydrotrope-Caged Cytochrome c with Boosted Stability in Harsh Environments: A Molecular Insight
<p>The input and main output files used for the paper <em><strong>"Nanostructured Hydrotropes Caged Cytochrome c with Boosted Stability in Harsh Environments: A Molecular Insights"</strong></em> are separated in the different tar files.</p> <p><strong>Contents:</strong></p> <p>00_packmol : box built using PACKMOL package for ATP, IL and ATP_IL systems</p> <p>01_Build_systems : parameters and input files for WAT, ATP, IL and ATP_IL systems</p> <p>02_Minimization_Equilibration_RT : minimization and equilibration inputs, restarts and output files for WAT, ATP, IL and ATP_IL systems at 300K</p> <p>03_Minimization_Equilibration_HT : minimization and equilibration inputs, restarts and output files for WAT, ATP, IL and ATP_IL systems at 363.15K</p> <p>04_HTMD_Cytc_WAT_RT : HTMD input, restarts and output files for Cyt c + WAT system at 300K</p> <p>05_HTMD_Cytc_ATP_RT : HTMD input, restarts and output files for Cyt c + ATP system at 300K</p> <p>06_HTMD_Cytc_IL_RT : HTMD input, restarts and output files for Cyt c + IL system at 300K</p> <p>07_HTMD_Cytc_ATP_IL_RT : HTMD input, restarts and output files for Cyt c + ATP_IL system at 300K</p> <p>08_HTMD_Cytc_WAT_HT : HTMD input, restarts and output files for Cyt c + WAT system at 363.15K</p> <p>09_HTMD_Cytc_ATP_HT : HTMD input, restarts and output files for Cyt c + ATP system at 363.15K</p> <p>10_HTMD_Cytc_IL_HT : HTMD input, restarts and output files for Cyt c + IL system at 363.15K</p> <p>11_HTMD_Cytc_ATP_IL_HT : HTMD input, restarts and output files for Cyt c + ATP_IL system at 363.15K</p> <p>12_HTMD_MD_analysis_RT : Analysis raw data for Bayesian MSM, RDF, RMSD, RMSF, H-bonds and Secondary structure changes at 300K </p> <p>13_HTMD_MD_analysis_HT : Analysis raw data for Bayesian MSM, RDF, RMSD, RMSF, H-bonds and Secondary structure changes at 363.15K </p> <p>14_H2O_RT : Radial Distribution Function (RDF) data for simulations in explicit water and in absence of the protein Cyt c</p> <p><strong>Notes:</strong> Each folder contains INFO.md with further detailed information on respective types of data.</p> <p> </p>
Fig. 3 in Serratene triterpenoids from Lycopodium cernuum L. as α-glucosidase inhibitors: Identification, structure-activity relationship and molecular docking studies
Fig. 3. SAR studies of isolates against α-glucosidase.
Fig. 2. 1H–1H in Serratene triterpenoids from Lycopodium cernuum L. as α-glucosidase inhibitors: Identification, structure-activity relationship and molecular docking studies
Fig. 2. 1H–1H COSY, Key HMBC and ROESY correlations of compounds 1–7.
Fig. 5 in Alkaloids from Lepidium meyenii (Maca), structural revision of macaridine and UPLC-MS/MS feature-based molecular networking
Fig. 5. Results of three channel MRM scans using UPLC conditions for the TQD system.
Fig. 1 in Alkaloids from Lepidium meyenii (Maca), structural revision of macaridine and UPLC-MS/MS feature-based molecular networking
Fig. 1. Structure of isolated imidazole, amidine and β-carboline alkaloids.
Fig. 3 in Alkaloids from Lepidium meyenii (Maca), structural revision of macaridine and UPLC-MS/MS feature-based molecular networking
Fig. 3. Structures of the proposed 'macaridine' (left) and macapyrrolin C (right).
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.