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Journal articles on the topic 'Structural assemblies'

Author: Grafiati

Published: 4 June 2021

Last updated: 26 July 2025

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1

Wick, Ryan R., and Kathryn E. Holt. "Benchmarking of long-read assemblers for prokaryote whole genome sequencing." F1000Research 8 (December 23, 2019): 2138. http://dx.doi.org/10.12688/f1000research.21782.1.

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Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled – one contig per chromosome or plasmid. However, the high per-read error rate of long-read sequencing necessitates different approaches to assembly than those used for short-read sequencing. Multiple assembly tools (assemblers) exist, which use a variety of algorithms for long-read assembly. Methods: We used 500 simulated read sets and 120 real read sets to assess the performance of six long-read assemblers (Canu, Flye, Mi

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2

Njike, Manette, Walter O. Oyawa, and Silvester O. Abuodha. "Structural Performance of Straw Block Assemblies under Compression Load." Open Construction & Building Technology Journal 14, no. 1 (2020): 350–57. http://dx.doi.org/10.2174/1874836802014010350.

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Background: In recent decades, the enduring interest and continued development of straw bale as a walling material are based on its beneficial properties. Straw bale is a biomaterial that contributes greatly to carbon footprint reduction and offers excellent thermal insulation. It is proved that plastered straw bale assemblies have good mechanical properties and can be used for the construction of a single storey building. It is known that straw bale presents high displacement in the assemblies; thus, pre-compression is a major step that helps to push down straw bale so as to avoid future stru

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3

Doerr, Allison. "Structural analysis of macromolecular assemblies." Nature Methods 5, no. 1 (2008): 23. http://dx.doi.org/10.1038/nmeth1160.

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4

Fujii, Shota, Rika Miyake, Liliana de Campo, Ji Ha Lee, Rintaro Takahashi, and Kazuo Sakurai. "Structural Polymorphism of Resorcinarene Assemblies." Langmuir 36, no. 22 (2020): 6222–27. http://dx.doi.org/10.1021/acs.langmuir.0c00861.

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5

Wick, Ryan R., and Kathryn E. Holt. "Benchmarking of long-read assemblers for prokaryote whole genome sequencing." F1000Research 8 (April 22, 2020): 2138. http://dx.doi.org/10.12688/f1000research.21782.2.

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Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled – one contig per chromosome or plasmid. However, the high per-read error rate of long-read sequencing necessitates different approaches to assembly than those used for short-read sequencing. Multiple assembly tools (assemblers) exist, which use a variety of algorithms for long-read assembly. Methods: We used 500 simulated read sets and 120 real read sets to assess the performance of seven long-read assemblers (Canu, Flye,

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6

Percec, Virgil. "Bioinspired supramolecular liquid crystals." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 364, no. 1847 (2006): 2709–19. http://dx.doi.org/10.1098/rsta.2006.1848.

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A brief account on the historical events leading to the discovery of self-assembling dendrons that generate self-organizable supramolecular dendrimers, or supramolecular polymers, and self-organizable dendronized polymers is provided. These building blocks were accessed by an accelerated design strategy that involves structural and retrostructural analysis of periodic and quasi-periodic assemblies. This design strategy mediated the discovery of porous helical supramolecular structures that self-assembled from dendritic dipeptides. Helical porous columns are the closest mimics of biologically r

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7

Fan, Dongxiao, Chen Yao, Wenya Zhou, and Xinsong Li. "Ultrashort Lipopeptides Self-Assembled with Gold Nanoparticles as Potent Antimicrobial Agents." Journal of Nanoscience and Nanotechnology 18, no. 12 (2018): 8124–32. http://dx.doi.org/10.1166/jnn.2018.16411.

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To develop new antimicrobial synthetic lipopeptides with optimizing peptide length, cationic tripeptides RWR/WRR were N-terminal fatty acylated, and self-assembled with 1-dodecanethiol-anchored gold nanoparticles (Au-DT NPs) via hydrophobic interaction. The ultrashort lipopeptides and their nano-assemblies were effective against a variety of microorganisms, with minimal inhibitory concentrations ranging from 0.5 to 8 μg/mL. Hemolysis analysis and in vitro cytotoxicity assay revealed that self-assembling with Au-DT NPs would improve biological toxicity of lipopeptides, especially for the most a

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8

Wick, Ryan R., and Kathryn E. Holt. "Benchmarking of long-read assemblers for prokaryote whole genome sequencing." F1000Research 8 (February 1, 2021): 2138. http://dx.doi.org/10.12688/f1000research.21782.4.

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Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled – one contig per chromosome or plasmid. However, the high per-read error rate of long-read sequencing necessitates different approaches to assembly than those used for short-read sequencing. Multiple assembly tools (assemblers) exist, which use a variety of algorithms for long-read assembly. Methods: We used 500 simulated read sets and 120 real read sets to assess the performance of eight long-read assemblers (Canu, Flye,

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9

Wick, Ryan R., and Kathryn E. Holt. "Benchmarking of long-read assemblers for prokaryote whole genome sequencing." F1000Research 8 (September 17, 2020): 2138. http://dx.doi.org/10.12688/f1000research.21782.3.

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Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled – one contig per chromosome or plasmid. However, the high per-read error rate of long-read sequencing necessitates different approaches to assembly than those used for short-read sequencing. Multiple assembly tools (assemblers) exist, which use a variety of algorithms for long-read assembly. Methods: We used 500 simulated read sets and 120 real read sets to assess the performance of eight long-read assemblers (Canu, Flye,

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10

Nakamura, Noriko, Yuki Mochida, Kazuko Toh, Shigeto Fukushima, Horacio Cabral, and Yasutaka Anraku. "Effect of Mixing Ratio of Oppositely Charged Block Copolymers on Polyion Complex Micelles for In Vivo Application." Polymers 13, no. 1 (2020): 5. http://dx.doi.org/10.3390/polym13010005.

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Self-assembled supramolecular structures based on polyion complex (PIC) formation between oppositely charged polymers are attracting much attention for developing drug delivery systems able to endure harsh in vivo environments. As controlling polymer complexation provides an opportunity for engineering the assemblies, an improved understanding of the PIC formation will allow constructing assemblies with enhanced structural and functional capabilities. Here, we focused on the influence of the mixing charge ratio between block aniomers and catiomers on the physicochemical characteristics and in

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11

Antson, Alfred A., Eleanor J. Dodson, and G. Guy Dodson. "Circular assemblies." Current Opinion in Structural Biology 6, no. 2 (1996): 142–50. http://dx.doi.org/10.1016/s0959-440x(96)80067-4.

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12

Rey, Félix A., and Helen Saibil. "Macromolecular assemblies." Current Opinion in Structural Biology 19, no. 2 (2009): 178–80. http://dx.doi.org/10.1016/j.sbi.2009.03.012.

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13

Rey, Felix A., and Wesley I. Sundquist. "Macromolecular assemblies." Current Opinion in Structural Biology 23, no. 2 (2013): 224–28. http://dx.doi.org/10.1016/j.sbi.2013.04.009.

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14

Chartrand, Daniel, and Garry Hanan. "Rhodium dimers as structural hubs for multichromophore assemblies." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1237. http://dx.doi.org/10.1107/s2053273314087622.

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Our main building blocks for forming supra-molecular assemblies of chromophoric units are the rhodium amidinate dimers. They offer an excellent structural backbone for rigid polynuclear assemblies with their paddle wheel motif and strongly bonded ligands. We already showed that with a well designed amidinate ligand with a pyridyl group up to four metallic centers can be attached to the dimer.[1,2] Two main approaches were used to extend these assemblies: the first is through Suzuki coupling reactions which allows for an extended ligand and a control on the number of pyridyl present on the dime

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15

Duckett, Drew J., Jack Sullivan, Stacy Pirro, and Bryan C. Carstens. "Genomic Resources for the North American Water Vole (Microtus richardsoni) and the Montane Vole (Microtus montanus)." Gigabyte 2021 (May 6, 2021): 1–13. http://dx.doi.org/10.46471/gigabyte.19.

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Voles of the genus Microtus are important research organisms, yet genomic resources are lacking. Such resources would benefit future studies of immunology, phylogeography, cryptic diversity, and more. We sequenced and assembled nuclear genomes from two subspecies of water vole (Microtus richardsoni) and from the montane vole (Microtus montanus). The water vole genomes were sequenced with Illumina and 10× Chromium plus Illumina sequencing, resulting in assemblies with ∼1600,000 and ∼30,000 scaffolds, respectively. The montane vole was also assembled into ∼13,000 scaffolds using Illumina sequenc

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16

Pieters, Bas J. G. E., Mark B. van Eldijk, Roeland J. M. Nolte, and Jasmin Mecinović. "Natural supramolecular protein assemblies." Chemical Society Reviews 45, no. 1 (2016): 24–39. http://dx.doi.org/10.1039/c5cs00157a.

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17

Günther, Lisa M., Jasper Knoester, and Jürgen Köhler. "Limitations of Linear Dichroism Spectroscopy for Elucidating Structural Issues of Light-Harvesting Aggregates in Chlorosomes." Molecules 26, no. 4 (2021): 899. http://dx.doi.org/10.3390/molecules26040899.

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Linear dichroism (LD) spectroscopy is a widely used technique for studying the mutual orientation of the transition-dipole moments of the electronically excited states of molecular aggregates. Often the method is applied to aggregates where detailed information about the geometrical arrangement of the monomers is lacking. However, for complex molecular assemblies where the monomers are assembled hierarchically in tiers of supramolecular structural elements, the method cannot extract well-founded information about the monomer arrangement. Here we discuss this difficulty on the example of chloro

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18

Polewski, Lukasz, Andreas Springer, Kevin Pagel, and Christoph A. Schalley. "Gas-Phase Structural Analysis of Supramolecular Assemblies." Accounts of Chemical Research 54, no. 10 (2021): 2445–56. http://dx.doi.org/10.1021/acs.accounts.1c00080.

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19

Nelson, Erik L., Dan L. Wheat, and David W. Fowler. "Structural Behavior of Wood Shear Wall Assemblies." Journal of Structural Engineering 111, no. 3 (1985): 654–66. http://dx.doi.org/10.1061/(asce)0733-9445(1985)111:3(654).

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20

Karathanasopoulos, Nikolaos, and Panagiotis Angelikopoulos. "Optimal structural arrangements of multilayer helical assemblies." International Journal of Solids and Structures 78-79 (January 2016): 1–8. http://dx.doi.org/10.1016/j.ijsolstr.2015.09.023.

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21

Vallat, Brinda, and Helen M. Berman. "Structural highlights of macromolecular complexes and assemblies." Current Opinion in Structural Biology 85 (April 2024): 102773. http://dx.doi.org/10.1016/j.sbi.2023.102773.

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22

Nguyen, Que Dan, Kosuke Kikuchi, Basudev Maity, and Takafumi Ueno. "The Versatile Manipulations of Self-Assembled Proteins in Vaccine Design." International Journal of Molecular Sciences 22, no. 4 (2021): 1934. http://dx.doi.org/10.3390/ijms22041934.

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Protein assemblies provide unique structural features which make them useful as carrier molecules in biomedical and chemical science. Protein assemblies can accommodate a variety of organic, inorganic and biological molecules such as small proteins and peptides and have been used in development of subunit vaccines via display parts of viral pathogens or antigens. Such subunit vaccines are much safer than traditional vaccines based on inactivated pathogens which are more likely to produce side-effects. Therefore, to tackle a pandemic and rapidly produce safer and more effective subunit vaccines

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23

Caron-Rousseau, Alexis, Pierre Blanchet, and Louis Gosselin. "Parametric Study of Lightweight Wooden Wall Assemblies for Cold and Subarctic Climates Using External Insulation." Buildings 12, no. 7 (2022): 1031. http://dx.doi.org/10.3390/buildings12071031.

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While externally insulated wall assemblies are widely recognized for their hygrothermal performance, few research projects have focused on the impact of shifting the entire wall insulation to the exterior side of a structural cavity in cold or subarctic climates or its effectiveness in terms of acoustic performance and airtightness. The objective of this study was to propose fully externally insulated assemblies that could be used in cold and subarctic climates by assessing the benefits of the hygrothermal performance of these assemblies and by achieving a comparable airtightness and sound tra

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24

Sali, Andrej, and Wah Chiu. "Macromolecular Assemblies Highlighted." Structure 13, no. 3 (2005): 339–41. http://dx.doi.org/10.1016/j.str.2005.02.010.

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25

Felix, Jan, Kedar Moharana, Steven Demunck, et al. "Plasticity and cooperativity of cytokine-receptor assemblies at the cell surface." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C405. http://dx.doi.org/10.1107/s2053273314095941.

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Hybrid approaches in structural biology have had a tremendous impact on our ability to tackle complex biological problems including large and flexible protein-protein assemblies. We have been employing creative combinations of X-ray crystallography, Small-angle X-ray Scattering (SAXS) and electron microscopy in conjunction with molecular interaction studies and cellular interrogation of the systems under study to elucidate the structural and mechanistic principles underlying diverse cytokine-receptor assemblies. Our studies have revealed the unexpected structural diversity of such assemblies,

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26

Bera, Santu, and Ehud Gazit. "Self-assembly of Functional Nanostructures by Short Helical Peptide Building Blocks." Protein & Peptide Letters 26, no. 2 (2019): 88–97. http://dx.doi.org/10.2174/0929866525666180917163142.

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The self-assembly of short peptide building blocks into well-ordered nanostructures is a key direction in bionanotechnology. The formation of &#946; -sheet organizations by short peptides is well explored, leading to the development of a wide range of functional assemblies. Likewise, many natural proteinaceous materials, such as silk and amyloid fibrils, are based on β-sheet structures. In contrast, collagen, the most abundant protein in mammals, is based on helical arrangement. Similar to &#946;-sheet structures, short helical peptides have been recently discovered to possess a divers

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27

Ramakrishna, V. Hosur, and Chugh Jeetender. "NMR advances towards structural characterization of huge protein assemblies." Journal of Indian Chemical Society Vol. 87, Jan 2010 (2010): 43–52. https://doi.org/10.5281/zenodo.5775397.

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Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai-400 005, India <em>E-mail :</em> hosur@tifr .res .in         Fax : 91-22-22804610 Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109 <em>Manuscript received 25 August 2009, accepted 26 August 2009</em> A majority of cellular functions are mediated through protein-protein interaction/association. However, large assemblies of megadalton size pose a great challenge to structural investigations either by X-ray

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28

van der Velde, Frank. "A spy to spy on a spy: From type to token representation with cell assemblies." Behavioral and Brain Sciences 22, no. 2 (1999): 306–7. http://dx.doi.org/10.1017/s0140525x99501829.

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The idea of representing words with cell assemblies is very appealing. However, syntactic sequences need to be represented as well. This cannot be done by using the activity levels of assemblies. Instead, structural relations and operations between assemblies are needed to achieve serial order in syntactic word strings.

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29

Jaudzems, Kristaps, Tatyana Polenova, Guido Pintacuda, Hartmut Oschkinat, and Anne Lesage. "DNP NMR of biomolecular assemblies." Journal of Structural Biology 206, no. 1 (2019): 90–98. http://dx.doi.org/10.1016/j.jsb.2018.09.011.

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30

Rozenfeld, Julio H. K., Evandro L. Duarte, Leandro R. S. Barbosa, and M. Teresa Lamy. "The effect of an oligonucleotide on the structure of cationic DODAB vesicles." Physical Chemistry Chemical Physics 17, no. 11 (2015): 7498–506. http://dx.doi.org/10.1039/c4cp05652c.

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An oligonucleotide induces the fusion of DODAB unilamellar vesicles into multilamellar assemblies. The structural and thermotropic properties of these assemblies resemble those of coagel phase DODAB bilayers.

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31

Walters, Kylie J., and Piero Crespo. "Editorial overview: Macromolecular assemblies: clues from structural insights." Current Opinion in Structural Biology 67 (April 2021): vi—viii. http://dx.doi.org/10.1016/j.sbi.2021.01.005.

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32

Ban, N. "Structural and functional studies of large macromolecular assemblies." Acta Crystallographica Section A Foundations of Crystallography 61, a1 (2005): c5—c6. http://dx.doi.org/10.1107/s0108767305099769.

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33

Cecot, Giacomo, Mathieu Marmier, Silvano Geremia, et al. "The Intricate Structural Chemistry of MII2nLn-Type Assemblies." Journal of the American Chemical Society 139, no. 24 (2017): 8371–81. http://dx.doi.org/10.1021/jacs.7b04861.

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34

Wallace, Benjamin J., and Helmut Krawinkler. "Small‐Scale Model Tests of Structural Steel Assemblies." Journal of Structural Engineering 115, no. 8 (1989): 1999–2015. http://dx.doi.org/10.1061/(asce)0733-9445(1989)115:8(1999).

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35

Hanein, Dorit. "Structural analysis of supramolecular assemblies by hybrid methods." Journal of Structural Biology 158, no. 2 (2007): 135–36. http://dx.doi.org/10.1016/j.jsb.2007.04.005.

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36

Hanein, Dorit, and Ron Milligan. "Structural analysis of supramolecular assemblies by hybrid methods." Journal of Structural Biology 184, no. 1 (2013): 1. http://dx.doi.org/10.1016/j.jsb.2013.09.014.

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37

Orlova, E. V., and H. R. Saibil. "Structural Analysis of Macromolecular Assemblies by Electron Microscopy." Chemical Reviews 111, no. 12 (2011): 7710–48. http://dx.doi.org/10.1021/cr100353t.

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38

Chow, Dar-chone, Lena Brevnova, Xiao-lin He, Monika M. Martick, Alex Bankovich, and K. Christopher Garcia. "A structural template for gp130-cytokine signaling assemblies." Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1592, no. 3 (2002): 225–35. http://dx.doi.org/10.1016/s0167-4889(02)00317-8.

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39

Wang, Ziqi, Peng Song, Florin Isvoranu, and Mark Pauly. "Design and structural optimization of topological interlocking assemblies." ACM Transactions on Graphics 38, no. 6 (2019): 1–13. http://dx.doi.org/10.1145/3355089.3356489.

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40

Fass, Deborah, and David J. Thornton. "Mucin networks: Dynamic structural assemblies controlling mucus function." Current Opinion in Structural Biology 79 (April 2023): 102524. http://dx.doi.org/10.1016/j.sbi.2022.102524.

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41

Courrier, Nicolas, Pierre-Alain Boucard, and Bruno Soulier. "Variable-fidelity modeling of structural analysis of assemblies." Journal of Global Optimization 64, no. 3 (2015): 577–613. http://dx.doi.org/10.1007/s10898-015-0345-9.

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42

Pan, Keyao, and Mark Bathe. "Modeling Secondary Structural Elements in Programmed DNA Assemblies." Biophysical Journal 110, no. 3 (2016): 183a. http://dx.doi.org/10.1016/j.bpj.2015.11.1022.

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43

Heinz, Dirk W., Manfred S. Weiss, and K. Ulrich Wendt. "Biomacromolecular Interactions, Assemblies and Machines: A Structural View." ChemBioChem 7, no. 1 (2005): 203–8. http://dx.doi.org/10.1002/cbic.200500459.

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44

Bernadó, Pau. "Low‐resolution structural approaches to study biomolecular assemblies." WIREs Computational Molecular Science 1, no. 2 (2011): 283–97. http://dx.doi.org/10.1002/wcms.15.

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45

Carugo, Oliviero. "A structural proteomics filter: prediction of the quaternary structural type of hetero-oligomeric proteins on the basis of their sequences." Journal of Applied Crystallography 40, no. 6 (2007): 986–89. http://dx.doi.org/10.1107/s0021889807041076.

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A protein chain can correspond to a monomeric protein or it can form, together with other chains, oligomeric assemblies, which can be either homo-oligomers or hetero-oligomers. In the latter case, the three-dimensional structure of the single protein chain is unlikely to be determined, since it will probably be difficult to express and crystallize. A computational method is presented here that allows one to predict if a chain participates in hetero-oligomeric assemblies, on the basis of its amino acid composition, with accuracy close to 80%. Such a technique should improve the success rate of

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46

Alrubaie, Murtada Abass A., Douglas J. Gardner, and Roberto A. Lopez-Anido. "Structural Performance of HDPE and WPC Lumber Components Used in Aquacultural Geodesic Spherical Cages." Polymers 12, no. 1 (2019): 26. http://dx.doi.org/10.3390/polym12010026.

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Based on previous research, a novel wood–plastic composite (WPC) lumber has shown potential to replace high-density polyethylene (HDPE) lumber in the construction of aquacultural geodesic spherical cage structures. Six HDPE and six WPC assemblies, which are representative of typical full-size cage dimensions, were fabricated by bolting pairs of triangular panel components made with connected struts. Half of the panel assemblies had a plastic-coated steel wire mesh to simulate the actual restraint in field applications of the cages. The objective of the research was to characterize the structur

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47

Yeates, Todd O., and Jennifer E. Padilla. "Designing supramolecular protein assemblies." Current Opinion in Structural Biology 12, no. 4 (2002): 464–70. http://dx.doi.org/10.1016/s0959-440x(02)00350-0.

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48

Vakser, Ilya A., and Andrzej Joachimiak. "Editorial overview: Macromolecular assemblies." Current Opinion in Structural Biology 55 (April 2019): iii—v. http://dx.doi.org/10.1016/j.sbi.2019.07.003.

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49

Zhang, Xiaodong, and Tom L. Blundell. "Editorial overview: Macromolecular assemblies." Current Opinion in Structural Biology 61 (April 2020): vi—viii. http://dx.doi.org/10.1016/j.sbi.2020.02.002.

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50

Liu, Jin, and Luhua Lai. "Editorial overview: Allosteric assemblies." Current Opinion in Structural Biology 62 (June 2020): vi—vii. http://dx.doi.org/10.1016/j.sbi.2020.03.009.

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