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706 results for “molecular complexes”
Figure 4 in Distribution and molecular differentiation of Culex pipiens complex species in the Middle and Eastern Black Sea Regions of Turkey
Figure 4. The phylogenetic tree is based on a 651-bp region of the Ace-2 gene from Culex pipiens. The tree was constructed using the maximum likelihood method, and bootstrap values are shown as numbers on the tree.
FIG. 12 in Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific
FIG. 12. Penial morphology in Cadlina spp. A. Cadlina sp. 3, MIMB47975. B. Cadlina umiushi, MIMB47996. C. Cadlina laevis, MIMB47963. Scale bars: A, C = 100 µm; A', B' = 50 µm; C = 200 µm; C' = 20 µm. РИС. 12. МорфологиЯ пениса Cadlina spp. A. Cadlina sp. 3, MIMB47975. B. Cadlina umiushi, MIMB47996. C. Cadlina laevis, MIMB47963. Масштабные линейки: A, C = 100 мкм; A', B' = 50 мкм; C = 200 мкм; C' = 20 мкм.
FIG. 11 in Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific
FIG. 11. Configuration of male and female reproductive organs in Cadlina spp., female gland mass removed. A. Cadlina laevis, MIMB47963. B. Cadlina umiushi, MIMB47996. C. Cadlina sp. 3, MIMB47975. D. Cadlina sp. 4, MIMB47978. E. Cadlina sp. 1, MIMB47971. F. Cadlina sp. 7, MIMB47981. G. Cadlina sp. 6, MIMB47980. Abbreviations: amp = ampulla; bc = bursa copulatrix; ps = penial sheath; pvd = prostatic vas deferens; rs = receptaculum seminis; va = vagina. Scale bar: 1 mm. РИС. 11. МорфологиЯ муЖских и Женских репродуктивных органов Cadlina spp., комплекс Женских ЖелеЗ удален. A. Cadlina laevis, MIMB47963. B. Cadlina umiushi, MIMB47996. C. Cadlina sp. 3, MIMB47975. D. Cadlina sp. 4, MIMB47978. E. Cadlina sp. 1, MIMB47971. F. Cadlina sp. 7, MIMB47981. G. Cadlina sp. 6, MIMB47980. СокраЩениЯ: amp = ампулла; bc = копулЯтивнаЯ сумка; ps = мешок пениса; pvd = простатический семЯпровод; rs = семЯприемник; va = вагина. МасштабнаЯ линейка: 1 мм.
FIG. 10 in Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific
FIG. 10. Buccal armature of Cadlina umiushi from the Sea of Japan (SEM). A. MIMB47995, radula. B. MIMB47995, anterior radular portion, rachidian and inner lateral teeth. C. MIMB47995, outer lateral teeth. D. MIMB47995, radula on odontophore. E. MIMB47995, labial cuticle. F. MIMB47995, labial cuticle elements. G. MIMB47996, radula. H. MIMB47996, rachidian and innermost lateral teeth. I. MIMB47996, outer lateral teeth. Scale bars: A = 500 µm; B, C, I = 50 µm; D, E, G = 200 µm; F = 10 µm; H = 20 µm. РИС. 10. Буккальное вооруЖение Cadlina umiushi иЗ Японского морЯ (СЭМ). А. MIMB47995, радула. B. MIMB47995, переднЯЯ часть радулы, центральные и внутренние латеральные Зубы. С. MIMB47995, внешние латеральные Зубы. D. MIMB47995, радула на одонтофоре. Е. MIMB47995, лабиальнаЯ кутикула. F. MIMB47995, Элементы лабиальной кутикулы. G. MIMB47996, радула. H. MIMB47996, центральные и внутренние латеральные Зубы. I. MIMB47996, внешние латеральные Зубы. Масштабные линейки: A = 500 мкм; B, C, I = 50 мкм; D, E, G = 200 мкм; F = 10 мкм; Н = 20 мкм.
FIG. 9 in Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific
FIG. 9. Buccal armature of Cadlina sp. 6 (MIMB47980, Shikotan Is., Sea of Okhotsk) and Cadlina sp. 5 (MIMB47979, Iturup Is., Sea of Okhotsk) (SEM). A. Cadlina sp. 6, anterior radular portion. B. Cadlina sp. 6, rachidian and inner lateral teeth. C. Cadlina sp. 6, rachidian and innermost lateral teeth. D. Cadlina sp. 6, middle radular portion. E. Cadlina sp. 6, outer lateral teeth. F. Cadlina sp. 6, rachidian and innermost lateral teeth. G. Cadlina sp. 6, radula on odontophore. H. Cadlina sp. 6, labial cuticle. I. Cadlina sp. 6, labial cuticle elements. J. Cadlina sp. 5, radula. K. Cadlina sp. 5, rachidian and inner lateral teeth. L. Cadlina sp. 5, rachidian teeth. M. Cadlina sp. 5, outer lateral teeth. N. Cadlina sp. 5, radula on odontophore. O. Cadlina sp. 5, labial cuticle. P. Cadlina sp. 5, labial cuticle rodlets. Scale bars: A, N, O = 100 µm; B, E, M = 50 µm; C, F, I, L = 10 µm; D, G, H, J = 200 µm; K, P = 20 µm. РИС. 9. Буккальное вооруЖение Cadlina sp. 6 (MIMB47980, о. Шикотан, Охотское море) и Cadlina sp. 5 (MIMB47979, о. Итуруп, Охотское море) (СЭМ). A. Cadlina sp. 6, переднЯЯ часть радулы. B. Cadlina sp. 6, центральные и внутренние латеральные Зубы. C. Cadlina sp. 6, центральные и внутренние латеральные Зубы. D. Cadlina sp. 6, среднЯЯ часть радулы. E. Cadlina sp. 6, внешние латеральные Зубы. F. Cadlina sp. 6, центральные и внутренние латеральные Зубы. G. Cadlina sp. 6, радула на одонтофоре. H. Cadlina sp. 6, лабиальнаЯ кутикула. I. Cadlina sp. 6, Элементы лабиальной кутикулы. J. Cadlina sp. 5, радула. К. Cadlina sp. 5, центральные и внутренние латеральные Зубы. L. Cadlina sp. 5, центральные Зубы. М. Cadlina sp. 5, внешние латеральные Зубы. N. Cadlina sp. 5, радула на одонтофоре. О. Cadlina sp. 5, лабиальнаЯ кутикула. P. Cadlina sp. 5, Элементы лабиальной кутикулы. Масштабные линейки: A, N, O = 100 мкм; B, E, M = 50 мкм; C, F, I, L = 10 мкм; D, G, H, J = 200 мкм; К, Р = 20 мкм.
FIG. 8 in Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific
FIG. 8. Buccal armature of Cadlina sp. 7 (MIMB47981, Sea of Japan) and Cadlina sp. 4 (MIMB47978, Sea of Japan) (SEM). А. Cadlina sp. 7, radula. B. Cadlina sp. 7, anterior radular portion, rachidian and inner lateral teeth. C. Cadlina sp. 7, outer lateral teeth. D. Cadlina sp. 7, rachidian and innermost lateral teeth. E. Cadlina sp. 4, radula. F. Cadlina sp. 4, anterior radular portion, rachidian and inner lateral teeth. G. Cadlina sp. 4, rachidian and innoermost lateral teeth. H. Cadlina sp. 4, outer lateral teeth. I. Cadlina sp. 4, labial cuticle rodlets. Scale bars: A = 300 µm; B, F = 100 µm; C = 30 µm; D = 10 µm; E = 400 µm; G, I = 20 µm; H = 50 µm. РИС. 8. Буккальное вооруЖение Cadlina sp. 7 (MIMB47981, Японское море) и Cadlina sp. 4 (MIMB47978, Японское море) (СЭМ). А. Cadlina sp. 7, радула. B. Cadlina sp. 7, переднЯЯ часть радулы, центральные и внутренние латеральные Зубы. C. Cadlina sp. 7, наруЖные латеральные Зубы. D. Cadlina sp. 7, центральные и внутренние латеральные Зубы. Е. Cadlina sp. 4, радула. F. Cadlina sp. 4, переднЯЯ часть радулы, центральные и внутренние латеральные Зубы. G. Cadlina sp. 4, переднЯЯ часть радулы, центральные и внутренние латеральные Зубы. H. Cadlina sp. 4, внешние латеральные Зубы. I. Cadlina sp. 4, Элементы лабиальной кутикулы. Масштабные линейки: A = 300 мкм; B, F = 100 мкм; С = 30 мкм; D = 10 мкм; Е = 400 мкм; G, I = 20 мкм; Н = 50 мкм.
FIG. 7 in Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific
FIG. 7. Buccal armature of Cadlina sp. 3 from the Sea of Japan (SEM). A. MIMB47975, radula. B. MIMB47975, anterior radular portion, rachidian and inner lateral teeth. C. MIMB47975, anterior radular portion, outer lateral teeth. D. MIMB47976, radula. E. MIMB47976, anterior radular portion, rachidian and inner lateral teeth. F. MIMB47976, anterior radular portion, outer lateral teeth. G. MIMB47976, odontophore with radula. H. MIMB47976, labial cuticle. I. MIMB47976, labial cuticle rodlets. J. MIMB47973, anterior radular portion, rachidian and inner lateral teeth. K. MIMB47973, anterior radular portion, outer lateral teeth. L. MIMB47973, labial cuticle rodlets. Scale bars: A, D, H = 500 µm; B, C, F, J = 50 µm; E = 100 µm; G = 200 µm; I, L = 10 µm; K = 20 µm. РИС. 7. Буккальное вооруЖение Cadlina sp. 3 иЗ Японского морЯ (SEM). А. MIMB47975, радула. B. MIMB47975, переднЯЯ часть радулы, центральные и внутренние латеральные Зубы. С. MIMB47975, переднЯЯ часть радулы, внешние латеральные Зубы. D. MIMB47976, радула. Е. MIMB47976, переднЯЯ часть радулы, центральные и внутренние латеральные Зубы. F. MIMB47976, переднЯЯ часть радулы, внешние латеральные Зубы. G. MIMB47976, одонтофор с радулой. Н. MIMB47976, лабиальнаЯ кутикула. I. MIMB47976, Элементы лабиальной кутикулы. J. MIMB47973, переднЯЯ часть радулы, центральные и внутренние латеральные Зубы. К. MIMB47973, переднЯЯ часть радулы, внешние латеральные Зубы. L. MIMB47973, Элементы лабиальной кутикулы. Масштабные линейки: A, D, H = 500 мкм; B, C, F, J = 50 мкм; Е = 100 мкм; G = 200 мкм; I, L = 10 мкм; К = 20 мкм.
FIG. 6 in Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific
FIG. 6. Buccal armature of Cadlina sp. 1 (MIMB47971, Urup Is., Sea of Okhotsk) and Cadlina sp. 2 (MIMB42230, Iturup Is., Sea of Okhotsk) (SEM). A. Cadlina sp. 1, radula. B. Cadlina sp. 1, anterior radular portion, rachidian and lateral teeth. C. Cadlina sp. 1, rachidian and innermost lateral teeth. D. Cadlina sp. 1, outer lateral teeth. E. Cadlina sp. 1, outer lateral teeth. F. Cadlina sp. 1, labial cuticle rodlets. G. Cadlina sp. 2, anterior radular portion, rachidian and inner lateral teeth. H. Cadlina sp. 2, outer lateral teeth. I. Cadlina sp. 2, labial cuticle rodlets. Scale bars: A = 500 µm; B = 300 µm; C = 50 µm; D, E = 100 µm; F = 20 µm; G, H = 30 µm; I = 10 µm. РИС. 6. Буккальное вооруЖение Cadlina sp. 1 (MIMB47971, о. Уруп, Охотское море) и Cadlina sp. 2 (MIMB42230, о. Итуруп, Охотское море) (СЭМ). А. Cadlina sp. 1, радула. B. Cadlina sp. 1, переднЯЯ часть радулы, центральные и внутренние латеральные Зубы. C. Cadlina sp. 1, центральные и внутренние латеральные Зубы. D. Cadlina sp. 1, внешние латеральные Зубы. Е. Cadlina sp. 1, внешние латеральные Зубы. F. Cadlina sp. 1, Элементы лабиальной кутикулы. G. Cadlina sp. 2, переднЯЯ часть радулы, центральные и внутренние латеральные Зубы. H. Cadlina sp. 2, внешние латеральные Зубы. I. Cadlina sp. 2, Элементы лабиальной кутикулы. Масштабные линейки: A = 500 мкм; B = 300 мкм; С = 50 мкм; D, Е = 100 мкм; F = 20 мкм; G, Н = 30 мкм; I = 10 мкм.
FIG. 5 in Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific
FIG. 5. Buccal armature of Cadlina laevis s.str., specimens from the White Sea (SEM). A. MIMB47939, radula. B. MIMB47939, anterior radular portion, rachidian and inner lateral teeth. C. MIMB47939, same as B, enlarged. D. MIMB47939, anterior radular portion, outer lateral teeth. E. MIMB47939, odontophore with radula. F. MIMB47939, labial cuticle. G. MIMB47939, labial cuticle rodlets. H. MIMB47963, radula. I. MIMB47963, middle radular portion, rachidian and inner lateral teeth. K. MIMB47963, middle radular portion, rachidian and innermost laterals. L. MIMB47963, outer lateral teeth. M. MIMB47963, odontophore with radula. N. MIMB47963, labial cuticle. O. MIMB47963, labial cuticle rodlets. Scale bars: A, E, H = 200 µm; B, D, I = 50 µm; C, K, L, N = 20 µm; F, M = 100 µm; G = 10 µm; O = 5 µm. РИС. 5. Буккальное вооруЖение Cadlina laevis s.str., особи иЗ Белого морЯ (СЭМ). A. MIMB47939, радула. B. MIMB47939, переднЯЯ часть радулы, центральные и внутренние латеральные Зубы. C. MIMB47939, то Же, что B, увеличенное. D. MIMB47939, переднЯЯ часть радулы, внешние латеральные Зубы. E. MIMB47939, одонтофор с радулой. F. MIMB47939, лабиальнаЯ кутикула. G. MIMB47939, родлеты лабиальной кутикулы. H. MIMB47963, радула. I. MIMB47963, среднЯЯ часть радулы, центральные и внутренние латеральные Зубы. K. MIMB47963, среднЯЯ часть радулы, центральные и внутренние латеральные Зубы. L. MIMB47963, наруЖные латеральные Зубы. М. MIMB47963, одонтофор с радулой. N. MIMB47963, лабиальнаЯ кутикула. O. MIMB47963, родлеты лабиальной кутикулы. Масштабные линейки: A, E, H = 200 мкм; B, D, I = 50 мкм; С, К, L, N = 20 мкм; F, М = 100 мкм; G = 10 мкм; О = 5 мкм.
FIG. 3 in Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific
FIG. 3. COI haplotype network of Cadlina laevis species complex produced with TCS method in PopART. Colours of circles refer to the geographic origin of each haplotype. The relative size of circles is proportional to the number of sequences of that same haplotype. РИС. 3. Сеть гаплотипов COI комплекса видов Cadlina laevis, полученнаЯ методом TCS в PopART. Цвета круЖков обоЗначают географическое происхоЖдение каЖдого гаплотипа. Относительный раЗмер круЖков пропорционален количеству последовательностей одного и того Же гаплотипа.
FIG. 4 in Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific
FIG. 4. Photos of studied specimens from different localities, all measurements are indicated in preserved state. A. Cadlina laevis, MIMB47953, White Sea, 16 mm in length. B. Cadlina laevis, MIMB47970, Barents Sea, 13 mm in length. C. Cadlina laevis, MIMB47948, White Sea, 10 mm in length. D. Cadlina laevis, MIMB47965, White Sea, 9 mm in length. E. Cadlina laevis, MIMB47958, White Sea, 10 mm in length. F. Cadlina sp. 1, MIMB47971, Urup Is., Sea of Okhotsk, 22 mm in length. G. Cadlina sp. 2, MIMB42230, Iturup Is., Sea of Okhotsk, 18 mm in length. H. Cadlina sp. 3, MIMB47974, Sea of Japan, 10 mm in length. I. Cadlina sp. 3, MIMB47972, Sea of Japan, 15 mm in length. K. Cadlina sp. 5, MIMB47979, Iturup Is., Sea of Okhotsk, 11 mm in length. L. Cadlina sp. 7, MIMB47981, Sea of Japan, 25 mm in length. M. Cadlina sp. 6, MIMB47980, Shikotan Is., Sea of Okhotsk, 29 mm in length. N. Cadlina umiushi, MIMB48000, Sea of Japan, 17 mm in length. РИС. 4. Фотографии иЗученных ЭкЗемплЯров иЗ раЗных регионов, раЗмер тела укаЗан длЯ фиксированного состоЯниЯ. А. Cadlina laevis, MIMB47953, Белое море, длина 16 мм. B. Cadlina laevis, MIMB47970, Баренцево море, длина 13 мм. C. Cadlina laevis, MIMB47948, Белое море, длина 10 мм. D. Cadlina laevis, MIMB47965, Белое море, длина 9 мм. E. Cadlina laevis, MIMB47958, Белое море, длина 10 мм. F. Cadlina sp. 1, MIMB47971, о. Уруп, Охотское море, длина 22 мм. G. Cadlina sp. 2, MIMB42230, о. Итуруп, Охотское море, длина 18 мм. H. Cadlina sp. 3, MIMB47974, Японское море, длина 10 мм. I. Cadlina sp. 3, MIMB47972, Японское море, длина 15 мм. К. Cadlina sp. 5, MIMB47979, о. Итуруп, Охотское море, длина 11 мм. L. Cadlina sp. 7, MIMB47981, Японское море, длина 25 мм. М. Cadlina sp. 6, MIMB47980, о. Шикотан, Охотское море, длина 29 мм. N. Cadlina umiushi, MIMB48000, Японское море, длина 17 мм.
FIG. 2 in Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific
FIG. 2. Maximum Likelihood phylogenetic tree based on the COI-based dataset, species-level clades and outgroups are collapsed to a single branch, except representatives of the Cadlina laevis species complex. Specimens studied in this work are highlighted in bold. Numbers above branches indicate posterior probabilities from Bayesian inference, numbers bellow branches show bootstrap supports from Maximum likelihood analysis. Blocks on the right indicate species delimitation results, number refers to respective operational taxonomical unit. Respective photographs of studied specimens are given on the right. РИС. 2. Филогенетическое дерево, построенное методом максимального правдоподобиЯ, основанное на выравнивании по гену COI, клады и внешние группы на уровне вида сколлапсированы в одну ветвь, За исключением представителей видового комплекса Cadlina laevis. ОбраЗцы, иЗученные в данной работе, выделены Жирным шрифтом. Числа над ветвЯми обоЗначают апостериорные вероЯтности байесовского аналиЗа, числа под ветвЯми покаЗывают бутстрепподдерЖку аналиЗа максимального правдоподобиЯ. Блоки справа обоЗначают реЗультаты тестов на определение видовых границ, номер относитсЯ к соответствуюЩей оперативной таксономической единице. Справа приведены фотографии иЗученных ЭкЗемплЯров.
FIG. 1 in Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific
FIG. 1. Map of the North-West Pacific and Russian Arctic representing collection sites and type localities of described species of the Cadlina laevis species complex. РИС. 1. Карта Северо-Западной части Тихого океана и Российской Арктики, с укаЗанием точек сбора и типовых местонахоЖдений описанных видов иЗ комплекса Cadlina laevis.
Reference data and analysis software for "Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane"
<p>Reference data set for the single molecule co-tracking analysis presented in "Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane". Corresponding author for further inquiries:</p> <p>Prof. Dr. Jacob Piehler</p> <p>University of Osnabrück, Department of Biology/Chemistry, Division of Biophysics, Barbarastr. 11, 49076 Osnabrück, Germany</p> <p>https://www.biophysik.uni-osnabrueck.de/</p>
Molecular data from "Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex)"
<p><strong>Phylogenetic_dataset.csv</strong>: Unfiltered DArTseq data used in phylogenetic analyses. Readable by 'dartR' (Gruber et al. 2018).</p> <p><strong>Population_dataset.csv</strong>: Unfiltered DArTseq data used in population-level analyses. Readable by 'dartR' (Gruber et al. 2018).</p> <p><strong>Reference.csv</strong>: Spreadsheet listing individuals included in molecular analyses. Includes vouchers, species, name of each sample in DArTseq data sets, and GenBank accession numbers (GB) for mitochondrial data. ABTC stands for Australian Biological Tissue Collection; AA and CCM for field numbers of uncatalogued specimens. Other collection acronyms follow Sabaj (2019). We refrain from assigning individuals that were not included in the molecular analyses to any given species.</p>
Data from: Leme et al. (2022) New genera and a new species in the "Cryptanthoid Complex" (Bromeliaceae: Bromelioideae) based on the morphology of recently discovered species, seed anatomy, and improvements in molecular phylogeny. Phytotaxa (doi: 10.11646/phytotaxa.544.2.2)
<p>DNA sequence alignments as well as the input and output files which specify the different data partitioning schemes used for phylogenetic analyses in Leme et al. (2022) New genera and a new species in the “Cryptanthoid Complex” (Bromeliaceae: Bromelioideae) based on the morphology of recently discovered species, seed anatomy, and improvements in molecular phylogeny. Phytotaxa. (doi: 10.11646/phytotaxa.544.2.2)</p>
Molecular dynamics simulations of an Ago2-RNA complex in different force fields
<p>This set of simulations contains 2us of Ago2-RNA complex in Amber ff14SB + OL3, ff19SB + OL3 and Desmond OPLS4 force fields. The polarizable force field AMOEBA has two simulation sets of 10*10ns and 2*100ns. The trajectories have been wrapped in the periodic box, centered around the protein atoms and the water molecules have been stripped out to conserve space using cpptraj. The trajectories are presented in Gromacs xtc-format which can be opened with the corresponding pdb file in multiple software tools such as VMD, PyMol or CaverAnalyst. The simulations are based on the crystal structure PDB ID 4W5O, where the missing loops were modeled using the Schrödinger Suite and missing nucleotides added manually. </p>
Molecular dynamics simulation trajectories of HIV protein gp120 in complex with antibody VRC01 and 30 of its Ala mutants
<p>This data set accompanies the publication by S. Conti, E. Lau, and V. Ovchinnikov entitled "On the rapid calculation of binding affinities for antigen and antibody design and affinity maturation simulations", to be published in the MDPI journal Antibodies. It contains molecular dynamics simulation trajectories of HIV protein gp120 in complex with antibody VRC01 and 30 of its Ala mutants, as described in the paper. The format of the trajectory files is CHARMM-compatible dcd. The files can be visualized with the program Visual Molecular Dynamics (VMD) (see paper by Humphrey et al. 1996, J. Molec. Graphics). The accompanying file "view" is a tcl-based script for VMD that can be executed in the Linux environment using: "vmd -e view", which will display the trajectory of the mutant specified by editing the first noncomment line of the script.<br> </p>
A dynamical view of protein-protein complexes: studies by molecular dynamics simulations
<p>All-atom MD simulations generated for the manuscript "A dynamical view of protein-protein complexes: studies by molecular dynamics simulations". Eight binary protein-protein complexes from the Docking benchmark and the Affinity benchmark are studied in this work: 2OOB (an ubiquitin/ubiquitin ligase complex), 1AY7 (a ribonuclease Sa/barstar complex), 1BRS (a barnase/barstar complex), 3SGB (a proteinase B/inhibitor), 1EMV (a colicin/immunity protein complex), 1PVH (complex between Interleukine 6 receptor and leukemia inhibitory factor), 1GCQ (Vav/GRB2 SH3 domains complex) and 1AK4 (cyclophilin/HIV capsid complex)</p> <p>Each folder for a binary complex is organised as followed:</p> <p>- in <strong>A</strong> and <strong>B</strong> there are the dry MD simulations for the unbound proteins</p> <p>- in <strong>complex</strong> there are two folders (<strong>without_water</strong> and <strong>water</strong>) where the dry simulation and the simulation with water molecules are provided</p>
Molecular dynamics simulation of SpoIVFB:Pro-SigmaK complex (in POPE/POPG mixture)
<p>Simulation in 2:1 POPE:POPG mixture.</p> <p>Found here are all files needed to reproduce or visualize the results of molecular dynamics simulation of the SpoIVFB intramembrane protease bound to the transcription factor Pro-sigmaK. The protein complex was embedded in a POPE:POPG bilayer using CHARMM-GUI and simulated using OpenMM. The README file is a C-shell script that will run equilibration and 250ns of unrestrained simulation. </p> <p>Individual output (.out) and trajectory (.dcd) files are provided for each checkpoint of the simulation. A combined trajectory containing 250 ns of unrestrained simulation is also provided (combined_250ns_traj.dcd). Together with the step5_input.psf file, this combined dcd file can be used with common software such as VMD to visualize the molecular dynamics trajectory.</p>
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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.