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About 10,000 papers for “Structural alignment”
Mahsa Alem (22446685), Seyyed Meysam Abtahi Froushani (5451077), Nasim Hajighahramani (22446688) et al. · Figshare · 2025
This file showcases different aspects of structural alignment between human HSPs and their bacterial counterparts. (XLSX)
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Cuncong Zhong, Haixu Tang, Shaojie Zhang · 2010
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Peter Naniima (114016), Eleonora Naimo (11648366), Sandra Koch (3944867) et al. · Figshare · 2021
<p>Structural alignment of the globular domains of HSV-1 pUL25 (PDB 2F5U), HCMV pUL77, KSHV pORF19, and MuHV-68 pORF19, obtained via a pairwise comparison with the Dali server [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3001423#pbio.3001423.ref037" target="_blank">37</a>]. Magenta or yellow background color indicates the SSE of the individual proteins as determined by the ENDscript server [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3001423#pbio.3001423.ref081" target="_blank">81</a>]; numbering and SSEs of HSV-1 pUL25 are shown above the alignment. Residues in red within black framed boxes are conserved across all 4 herpesvirus orthologs. Lowercase letters denote insertions relative to HSV-1 pUL25. Residues mutated in this study to block pentamerization are colored and framed in cyan and the positively charged residues in the funnel region of the pentameric pORF19<sub>KCTD</sub> in blue. HCMV, human cytomegalovirus; HSV, herpes simplex virus; KSHV, Kaposi’s sarcoma-associated herpesvirus; MuHV-68, murid gammaherpesvirus 68; SSE, secondary structure element.</p> <p>(TIF)</p>
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Stella Christie, Dedre Gentner, Stella Christie et al. · 2010
This article may be used for research, teaching and private study purposes. Any substantial or systematic reproduction, re-distribution, re-selling, loan or sub-licensing, systematic supply or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. The accuracy of any instructions, formulae and drug doses should be independently verified with primary sources. The publisher shall not be liable for any loss, actions, claims, proceedings, demand or costs or damages whatsoever or howsoever caused arising directly or indirectly in connection with or arising out of the use of this material. JOURNAL OF COGNITION AND DEVELOPMENT, 11(3):356–373 Copyright # 2010 Taylor &amp; Francis Group, LLC ISSN: 1524-8372 print=1532-7647 online
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Yvonne Resch (3070476), Katharina Blatt (186249), Ursula Malkus (3070461) et al. · Figshare · 2016
<p>(A) Alignment of predicted secondary structure elements of Der p 18 with the secondary structure of human chitinase (1wawA) for portions of human chitinase with known three-dimensional structure and of the Der p 18 putative chitin-binding domain with tachycitin (1dqcA) as created with the SWISS-MODEL program. Identical amino acids are indicated by dots, dashes represent gaps and similar secondary structure elements (β-strands, α-helices) are marked. (B) Structural model of Der p 18 generated by the SWISS-MODEL program. The 29-amino-acid connecting sequence is indicated by a continuous line.</p>
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Layal Kazma · 2006
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Nisith R. Mandal · Springer series on naval architecture, marine engineering, shipbuilding and shipping/Springer series on naval architecture, marine engineering, shipbuildung and shipping · 2016
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Nawder Loswin Loswin · Zenodo (CERN European Organization for Nuclear Research) · 2026
A minimal, architecture‑agnostic structural framework aligning atomic timekeeping with Resonance‑Time (RT) and Validated Spacetime (vST). The paper introduces a triadic decomposition of atomic clock architectures, a resonance‑based definition of the second, structural drift‑detection invariants, and a non‑disruptive roadmap for adoption. Fully compatible with existing SI standards.
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Nawder Loswin Loswin · Zenodo (CERN European Organization for Nuclear Research) · 2026
A minimal, architecture‑agnostic structural framework aligning atomic timekeeping with Resonance‑Time (RT) and Validated Spacetime (vST). The paper introduces a triadic decomposition of atomic clock architectures, a resonance‑based definition of the second, structural drift‑detection invariants, and a non‑disruptive roadmap for adoption. Fully compatible with existing SI standards.
Cited by 0Open access
Sana Waqar (20636487), Aamira Tariq (606502), Ubaid ullah (20636490) et al. · Figshare · 2025
<b>(A).</b>Structural superposition of ArsB <i>Klebsiella oxytoca</i> and <i>E</i>.<i>coli</i> using TM-align (<a href="https://zhanggroup.org/TM-align/" target="_blank">https://zhanggroup.org/TM-align/)</a>) showed 96%identical folding indicating high structural similarity with 1.26 RMSD (root mean square deviation) value. <b>(B).</b>Structural superposition of ArsB <i>Klebsiella oxytoca</i> and <i>Klebsiella pneumoniae</i> using TM-align (<a href="https://zhanggroup.org/TM-align/" target="_blank">https://zhanggroup.org/TM-align/)</a>) showed 96%identical folding indicating high structural similarity with 1.26 RMSD (root mean square deviation) value. <b>(C).</b> Structural superposition of ArsB <i>Klebsiella oxytoca</i> and <i>P</i>.<i>putida</i> using TM-align (<a href="https://zhanggroup.org/TM-align/" target="_blank">https://zhanggroup.org/TM-align/)</a>) showed 91.3%identical folding indicating comparatively less structural similarity with 2.06 RMSD (root mean square deviation) value.
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Ajay Singh Tanwar (478853), Venuka Durani Goyal (478854), Deepanshu Choudhary (478855) et al. · Figshare · 2013
<p>StPurL (PDB file 1T3T) in green color, TmPurQ (PDB file 3D54) in cyan color, IGP synthase (PDB file 1GPW) in salmon color, CPS (PDB file 1C30) in magenta color and GMP synthase (PDB file 1GPM) in yellow color. Secondary structure elements are labeled as per StPurL structure. Active site is demarcated by Cys-glutamine intermediate of StPurL and TmPurQ and inhibitor trapped in IGP synthase shown in sticks. The location of the xenon atom in the StPurL-Xenon complex is shown in an orange sphere and residues blocking the xenon binding pocket in CPS, IGP synthase and GMP synthase are shown in sticks.</p>
Cited by 0Open access
Galip Gürkan Yardımcı · Sabanci University · 2007
Understanding the structural means of protein function via structural comparisons have wide range of applications such as protein fold classification, protein structure modelling and design. In this thesis, a novel structural alignment algorithm based on a amino acid network model is presented. The method we present models proteins as an amino acid network, derived from contact map representation of proteins. By using this model, we obtain fast tertiary structure comparisons, and combine them with primary and secondary structure comparisons to develop an overall similarity function. The similarity function drives a dynamic programming based alignment algorithm to obtain fast and accurate structural alignments. The structural alignments obtained are used to discover functional structural subunits called domains and to discover overall structural similarity of two proteins. We compared our domain prediction results with existing domain recognition methods and saw that our method correlates well with existing methods. Our global structural alignment results are compared with CE alignments.
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Han, Buhm, Dost, Banu, Bafna, Vineet et al. · Journal of International Crisis and Risk Communication Research · 2008
In this paper, we address the problem of discovering novel non-coding RNA (ncRNA) using primary sequence, and secondary structure conservation, focusing on ncRNA families with pseudoknotted structures. Our main technical result is an efficient algorithm for computing an optimum structural alignment of an RNA sequence against a genomic substring. This algorithm has two applications. First, by scanning a genome, we can identify novel (homologous) pseudoknotted ncRNA, and second, we can infer the secondary structure of the target aligned sequence. We test an implementation of our algorithm (PAL) and show that it has near-perfect behavior for predicting the structure of many known pseudoknots. Additionally, it can detect the true homologs with high sensitivity and specificity in controlled tests. We also use PAL to search entire viral genome and mouse genome for novel homologs of some viral and eukaryotic pseudoknots, respectively. In each case, we have found strong support for novel homologs. © Mary Ann Liebert, Inc. 2008.
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Lorenzo Cecutti, Spike W.S. Lee · Research Square · 2022
Abstract Raising one's jammed fist is not just a common pictorial representation of struggle against the establishment but turns out to reflect a deeper connection between sensorimotor states and beliefs. The present research investigated how physical firmness, manipulated through muscle tightening, might shape beliefs. The central hypothesis, structural alignment, was tested against two other competing predictions: content extremity and content matching. Three studies provided evidence supporting structural alignment but not content matching or extremity. Specifically, the correlation between intelligence and personality lay beliefs (Studies 1-2), and the correlation between individualizing and binding moral foundations (Study 3) increased when participants jammed their fist (Study 1) or clenched their jaw (Studies 2-3). These effects emerged in the absence of mean-level differences (which would have reflected content matching or extremity). Moreover, they did not seem attributable to response bias or tiredness. Overall, sensorimotor experiences such as physical firmness can align higher-order cognitions such as beliefs in ways that are distinct from prior demonstrations of embodied cognition effects.
Cited by 0Open access
Journal of International Crisis and Risk Communication Research · 2008
In this paper, we address the problem of discovering novel non-coding RNA (ncRNA) using primary sequence, and secondary structure conservation, focusing on ncRNA families with pseudoknotted structures. Our main technical result is an efficient algorithm for computing an optimum structural alignment of an RNA sequence against a genomic substring. This algorithm has two applications. First, by scanning a genome, we can identify novel (homologous) pseudoknotted ncRNA, and second, we can infer the secondary structure of the target aligned sequence. We test an implementation of our algorithm (PAL) and show that it has near-perfect behavior for predicting the structure of many known pseudoknots. Additionally, it can detect the true homologs with high sensitivity and specificity in controlled tests. We also use PAL to search entire viral genome and mouse genome for novel homologs of some viral and eukaryotic pseudoknots, respectively. In each case, we have found strong support for novel homologs.
Cited by 0Open access
Xu Yang (112496), Hae Ryung Chang (791373), Y. Whitney Yin (791374) · Figshare · 2015
<p>(A). a T7 RNAP initiation complex showing the 17 bp promoter (purple) is recognized by AT-rich minor groove recognition loop, the intercalating hairpin and the specificity loop (all colored green). The NTD (yellow) and CTD (blue) are indicated. (B). Primary sequence and secondary structure of the NTD of Rpo41 indicating the deletion sites. A sequence alignment of T7 RNAP with the human and yeast mitochondrial RNAPs is presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136879#pone.0136879.s001" target="_blank">S1 Fig</a> (C). Purities of the Mtf1 and Rpo41 variants analyzed by SDS-PAGE.</p>
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Janet Bourne · 2025
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Encyclopedia of New Venture Management · 2012
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Thomas K. F. Wong, Kwok-Lung Wan, Bay-Yuan Hsu et al. · Bioinformatics · 2011
http://www.bio8.cs.hku.hk/RNASAlign.
Cited by 5Open access
Buhm Han, Banu Dost, Vineet Bafna et al. · Journal of Computational Biology · 2008
In this paper, we address the problem of discovering novel non-coding RNA (ncRNA) using primary sequence, and secondary structure conservation, focusing on ncRNA families with pseudoknotted structures. Our main technical result is an efficient algorithm for computing an optimum structural alignment of an RNA sequence against a genomic substring. This algorithm has two applications. First, by scanning a genome, we can identify novel (homologous) pseudoknotted ncRNA, and second, we can infer the secondary structure of the target aligned sequence. We test an implementation of our algorithm (PAL) and show that it has near-perfect behavior for predicting the structure of many known pseudoknots. Additionally, it can detect the true homologs with high sensitivity and specificity in controlled tests. We also use PAL to search entire viral genome and mouse genome for novel homologs of some viral and eukaryotic pseudoknots, respectively. In each case, we have found strong support for novel homologs.
Cited by 40Open access