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221 results for “Structural Biology”
Protein structure files for the paper "Multiplexed identification of RAS paralog imbalance as a driver of lung cancer growth" in Nature Cell Biology by Tang et al.
<p>This archive contains models of HRAS, KRAS, and NRAS homo- and heterodimers with various mutations discussed in the paper, "Multiplexed identification of RAS paralog imbalance as a driver of lung cancer growth" in Nature Cell Biology by Tang et al.<br> as well as crystallographic dimers of these proteins as identified by the ProtCAD database, http://dunbrack2.fccc.edu/ProtCAD/Results/PfamArchClusterInfo.aspx?GroupId=8 (cluster 5). Several of the models are shown in Supp. Figure 11b and the crystallographic dimers of RAS that provide evidence for the possible biological relevance of these models are shown in Supp. Figure 11a.</p> <p>The crystallographic dimers were identified by clustering all possible interfaces generated by symmetry operators in crystals of HRAS, KRAS, and NRAS as described in the paper: Xu, Q., Dunbrack, R.L. ProtCID: a data resource for structural information on protein interactions. <em>Nat Commun</em> <strong>11</strong>, 711 (2020). https://doi.org/10.1038/s41467-020-14301-4.</p> <p>The models were created by superposing monomers of HRAS, KRAS, or NRAS onto the alpha4-alpha5 dimer present in the crystal of PDB entry 3k8y. Mutations were made in PyMOL. The structures were relaxed with the FastRelax protocol and the Ref2015 scoring function in the program Rosetta, which uses the backbone-dependent rotamer library of Shapovalov and Dunbrack to repack side chains.</p> <p>The crystallographic dimers are contained in a zipped PyMOL session. The mmCIF format for all the structures is present in a zip file, Tang_et_al_crystallographic_and_modeled_RAS_dimer_ciffiles.zip. The PyMOL session and zip file contains 87 HRAS dimers, 14 KRAS dimers, and 1 NRAS dimer, all having the interface consisting of the alpha4 and alpha5 helices. The PyMOL session also contains the modeled structures. Only Mg ions and GTP/GNP/GDP ligands are shown. Others are present but hidden and may be displayed by PyMOL ("show sticks, het").</p> <p> </p>
MCR LTER: Coral Reef: Community structure outdoor flume data in support of Edmunds 2019 Marine Biology
This dataset contains data in support of Edmunds, P.J., S.S. Doo, R.C. Carpenter, 'Changes in coral reef community structure in response to year-long incubations under contrasting pCO2 regimes', Marine Biology, 2019, doi:10.1007/s00227-019-3540-2. Here, the effects of ocean acidification (OA) on back reef communities from Mo'orea, French Polynesia (17.492S, 149.826W), were tested from 12 November 2015 to 16 November 2016 in outdoor flumes maintained at various mean pCO2 levels. Change in mass and percent cover were recorded monthly. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2018). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.
Fig. 3 in Population structure and reproductive biology of Haemulopsis corvinaeformis (Perciformes, Haemulidae) in the south coast of Pernambuco, northeastern Brazil
Fig. 3. Monthly average (±SD) of the total length (TL, cm) of males, females and pooled sexes of Roughneck Grunt, Haemulopsis corvinaeformis (Steindachner, 1868), captured from August 2011 to July 2012, off the coast of state of Pernambuco, northeastern Brazil. Different letters indicate significant size differences between months for pooled sexes (∗, significant sizes differences between males and females; ∗∗, significant differences in sexual ratio).
Fig. 5 in Population structure and reproductive biology of Haemulopsis corvinaeformis (Perciformes, Haemulidae) in the south coast of Pernambuco, northeastern Brazil
Fig. 5. Total length at first sexual maturity (L 50, cm) and confidence interval (IC, 95%) for females, males and pooled sexes of Roughneck Grunt, Haemulopsis corvinaeformis (Steindachner, 1868), captured from August 2011 to June 2012, off the coast of state of Pernambuco, northeastern Brazil.
Fig. 4 in Population structure and reproductive biology of Haemulopsis corvinaeformis (Perciformes, Haemulidae) in the south coast of Pernambuco, northeastern Brazil
Fig. 4. Bimonthly changes in GSI (± standard error) and frequency of the different gonadal stages for Roughneck Grunt, Haemulopsis corvinaeformis (Steindachner, 1868), captured from August 2011 to June 2012, off the coast of state of Pernambuco, northeastern Brazil (A, immature; B, maturing; C, mature; D, spawned or resting). The numbers above the line represent the sample size of GSI analysis in each bimester.
Fig. 2 in Population structure and reproductive biology of Haemulopsis corvinaeformis (Perciformes, Haemulidae) in the south coast of Pernambuco, northeastern Brazil
Fig. 2. Absolute frequency distribution per length classes of males, females and pooled sexes for Roughneck Grunt, Haemulopsis corvinaeformis (Steindachner, 1868) captured from August 2011 to July 2014, off the coast of State of Pernambuco, northeastern Brazil. The vertical line represents the L50.
Fig. 1 in Population structure and reproductive biology of Haemulopsis corvinaeformis (Perciformes, Haemulidae) in the south coast of Pernambuco, northeastern Brazil
Fig. 1. Study area in the coast of state of Pernambuco, northeastern Brazil. Black dots represent fishing sites.
Fig. 6 in Structural biology and evolution in the monotypic Amazonian palm Wendlandiella (Arecoideae: Chamaedoreeae)
Fig. 6. – Pistillate flower of Wendlandiella gracilis. A. Pistillate flower at anthesis (var. gracilis); B. Upper view of pistillate flower (var. polyclada); C. Gynoecium (var. polyclada); D. Corolla and gynoecium (var. polyclada); E. Flower bud, LS (var. polyclada); F. Flower bud, TS (var. polyclada).
Fig. 7 in Structural biology and evolution in the monotypic Amazonian palm Wendlandiella (Arecoideae: Chamaedoreeae)
Fig. 7. – Fruits and seeds of Wendlandiella gracilis. A. Ripe fruit (var. gracilis); B. Ripe fruit (var. simplicifrons); C. Seed (var. gracilis). [Plant cultivated by H. Lorenzi in the Instituto Plantarum Botanical Garden, Campinas, Brazil] [Photos: A–B: H. Lorenzi; C: M. Caixeta]
Fig. 5 in Structural biology and evolution in the monotypic Amazonian palm Wendlandiella (Arecoideae: Chamaedoreeae)
Fig. 5. – Staminate flower in Wendlandiella gracilis. A. Anthesis (var. polyclada); B. Androecium displaying filaments and anthers (var. gracilis); C. Pistillode (var. gracilis); D. Calyx (var. gracilis); E. TS at basal level (var. polyclada); F. Pollen intermixed with raphide idioblasts (var. gracilis).
Fig. 2 in Structural biology and evolution in the monotypic Amazonian palm Wendlandiella (Arecoideae: Chamaedoreeae)
Fig. 2. – Root anatomy in Wendlandiella gracilis var. polyclada. A. Apex of the root, LS; B. Elongation area of root tip, CS; C. First order root, detail of raphide idioblasts, CS; D. First order root, detail of inner cortex starch containing cells, LS-CS.; E. Rhizodermis and exodermis, CS; F. Vascular cylinder and endodermis layer, CS. [Abbreviations: en, endodermis; ex, exodermis; fi, fiber; ic, inner cortex; me, meristematic zone; oc, outer cortex; pc, pith vascular cylinder; pe, pericycle; ph, phloem; rc, root cap; rh, rhizoderm; ri, raphide idioblast; vc, vascular cylinder; xy, xylem]
Fig. 3 in Structural biology and evolution in the monotypic Amazonian palm Wendlandiella (Arecoideae: Chamaedoreeae)
Fig. 3. – Leaf morphology and anatomy in Wendlandiella gracilis. A. Leaf morpho-types: var. gracilis: 1. adaxial side, 2. abaxial side; var. polyclada: 3. adaxial side, 4. abaxial side; var. simplicifrons: 5. adaxial side, small-leaved morpho-type, 6. adaxial side, large-leaved morpho-type; B. Leaf blade stomata, abaxial side; C. Leaf blade surface, abaxial side; D. Lamina anatomy (var. polyclada), CS. [Abbreviations: ep, epidermis; fi, fiber bundles in contact with epidermal layer; mc, mesophyll cells with chloroplasts; mr, midrib; ri, raphide idioblast; vs, vascular bundles free of surface layers]
Fig. 4 in Structural biology and evolution in the monotypic Amazonian palm Wendlandiella (Arecoideae: Chamaedoreeae)
Fig. 4. – Inflorescence structure and flower arrangements in Wendlandiella gracilis. A. 1-order ramification; B. Proximal ramification in basal rachillae; C. 2-branched order ramification in basal rachillae; D. Solitary female flowers (var. polyclada); E. Male flowers in an acervulus of two alternating rows (var. gracilis); F. Male flowers in an unordered acervulate complex (var. gracilis).
Fig. 1 in Structural biology and evolution in the monotypic Amazonian palm Wendlandiella (Arecoideae: Chamaedoreeae)
Fig. 1. – Growth habit diversity in Wendlandiella gracilis. A. Schematic representation of the development of stems and major types of growth habit; B. Solitary growth habit (var. simplicifrons); C. Clustered growth habits (var. gracilis); D. Production of new plantlets from aerial stems (var. simplicifrons). [B: Balslev et al., 7677, AAU; C: Balslev et al., 7865, AAU] [Photos: B, C: H. Balslev; D: S. Zona, taken in Nongnooch Tropical Garden, Pattaya, Thailand]
Fig. 4 in Structural biology and evolution in the monotypic Amazonian palm Wendlandiella (Arecoideae: Chamaedoreeae)
Fig. 4. – Inflorescence structure and flower arrangements in Wendlandiella gracilis. A. 1-order ramification; B. Proximal ramification in basal rachillae; C. 2-branched order ramification in basal rachillae; D. Solitary female flowers (var. polyclada); E. Male flowers in an acervulus of two alternating rows (var. gracilis); F. Male flowers in an unordered acervulate complex (var. gracilis). [Abbreviations: fRae, fertile rachillae; pb, peduncular bract; py, prophyll; sh, sheath; sRae, sterile rachillae]
Fig. 5 in Structural biology and evolution in the monotypic Amazonian palm Wendlandiella (Arecoideae: Chamaedoreeae)
Fig. 5. – Staminate flower in Wendlandiella gracilis. A. Anthesis (var. polyclada); B. Androecium displaying filaments and anthers (var. gracilis); C. Pistillode (var. gracilis); D. Calyx (var. gracilis); E. TS at basal level (var. polyclada); F. Pollen intermixed with raphide idioblasts (var. gracilis). [Abbreviations: aS, alternating stamens; fi, filament; oS, opposite stamens; pD, pistillode; pe, petal; ri, raphide idioblast; vb, vascular bundle]
Screening routine for integrative dynamic structural biology using SAXS and intramolecular FRET and DEER-EPR on hGBP1 (human guanalyte binding protein 1)
<p>Initial and selected ensemble for major and minor species of the human guanalyte binding protein 1 with scripts for the reading routine to combine and analyse jointly SAXS, EPR and FRET data.</p>
Data and code repository for Science Advances submission: Uncovering the biological basis of control energy: structural and metabolic correlates of energy inefficiency in temporal lobe epilepsy
<p>Data and codes related to the findings reported in the manuscript, "Uncovering the biological basis of control energy: structural and metabolic correlates of energy inefficiency in temporal lobe epilepsy", are deposited. Please refer to the notes located within each folder for further descriptions.</p>
Serum albumin domain structures in human blood serum by mass spectrometry and computational biology
<p>Contact prediction data generated by EPC-map used in the paper "Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology" by Rappsilber et al.</p>
Figure 2 in Endemic and enigmatic: the reproductive biology of Aegla (Crustacea: Anomura: Aeglidae) with observations on sperm structure
Figure 2. Light micrographs of Aegla rostrata Jara, 1977. A, Spermatophoric lobes; B–G, Squash of spermatophoric lobe contents showing spermatozoa (arrowheads) scattered amongst assorted cells (Asterisk in E and G indicate individual spermatozoa with three microtubular arms).
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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.