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SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments

Conan K. Wang, Ursula Broder, Saroja K. Weeratunga, Robin B. Gasser, Alex Loukas, Andreas Hofmann
<span title="2012-02-12">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
We have developed SBAL, a tool to generate and edit secondary structure-based sequence alignments. It is easy to install and provides a user-friendly interface.  ...  The algorithm implemented for automated and semiautomated secondary structure-based alignment calculations shows a comparable performance to existing software.  ...  We acknowledge partial support of this study by the ARC (to RG, AH and AL) and the NHMRC (to AH). Conflict of interest: none declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts035">doi:10.1093/bioinformatics/bts035</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22332239">pmid:22332239</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uvrt5e6jtbaetoknk4zc22kbxm">fatcat:uvrt5e6jtbaetoknk4zc22kbxm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20181101134604/https://research-repository.griffith.edu.au/bitstream/handle/10072/45823/74922_1.pdf;jsessionid=FA83A7FF3D07BB064583430F3577ADA9?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f5/70/f5709e4f7e8c646499641bec59c3d62bf0d5651f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts035"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

An integrated Java tool for generating amino acid sequence alignments with mapped secondary structure elements

Conan K. Wang, Andreas Hofmann
<span title="2014-05-20">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/by5shwibsvfk3acyvniuab5bra" style="color: black;">3 Biotech</a> </i> &nbsp;
Here, we report recent updates to the Java application SBAL, an integrated tool to generate, edit, visualise and analyse secondary structure-based sequence alignments.  ...  Keywords Modelling Á Structure analysis Á Structure-based amino acid sequence alignments Electronic supplementary material The online version of this article (  ...  and the source are credited.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s13205-014-0222-0">doi:10.1007/s13205-014-0222-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28324365">pmid:28324365</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4327748/">pmcid:PMC4327748</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ga7ghg3ndfez7jvxkwnpfevdxe">fatcat:ga7ghg3ndfez7jvxkwnpfevdxe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180725094504/https://link.springer.com/content/pdf/10.1007%2Fs13205-014-0222-0.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/58/a3/58a38699e56dfb6d9eac0ddbc05a3c98e9dddd41.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s13205-014-0222-0"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4327748" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Chemical probing suggests redox-regulation of the carbonic anhydrase activity of mycobacterial Rv1284

Lisa Nienaber, Elysia Cave-Freeman, Megan Cross, Lyndel Mason, Ulla-Maja Bailey, Parisa Amani, Rohan A. Davis, Paul Taylor, Andreas Hofmann
<span title="2015-05-18">2015</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6sl6l3ojendhnjf3odmmtutouq" style="color: black;">The FEBS Journal</a> </i> &nbsp;
These authors made equal contributions to the work Database Atomic coordinates and structure factors have been deposited with the PDB, accession numbers 4yf4, 4yf5, 4yf6.  ...  The active site cavity of this dimeric protein is characterised by an exceptionally small volume and harbours a catalytic zinc ion coordinated by two cysteine and one histidine residue side chains.  ...  MC and AH collected diffraction data, and AH solved the crystal structures. RAD provided natural products. PA, RAD, PT and AH analysed data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/febs.13313">doi:10.1111/febs.13313</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25929542">pmid:25929542</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x3lt27ag65ahtpbuisgxucqxdq">fatcat:x3lt27ag65ahtpbuisgxucqxdq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724114227/https://www.research.ed.ac.uk/portal/files/57303763/Chemical_probing_suggests_AAM.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1b/64/1b6474b59e7cc2d073cd1b8c8cd204f09ca77d4d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/febs.13313"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Evolutionary Relationship of Disease Resistance Genes in Soybean and Arabidopsis Specific for thePseudomonas syringaeEffectors AvrB and AvrRpm1

Tom Ashfield, Thomas Redditt, Andrew Russell, Ryan Kessens, Natalie Rodibaugh, Lauren Galloway, Qing Kang, Ram Podicheti, Roger W. Innes
<span title="2014-07-17">2014</span> <i title="American Society of Plant Biologists (ASPB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lyouqq67dncvxgcbflq26svwta" style="color: black;">Plant Physiology</a> </i> &nbsp;
The tightly linked soybean Rpg1b and Rpg1r genes share a close evolutionary relationship, with Rpg1b containing a recombination event that combined a NB domain closely related to Rpg1r with CC and LRR  ...  Using structural modeling, we mapped polymorphisms between Rpg1b and Rpg1r onto the predicted tertiary structure of Rpg1b, which revealed highly polymorphic surfaces within both the CC and LRR domains.  ...  ACKNOWLEDGEMENTS We thank Michelle Metcalf and Brian Rutter for technical assistance, Blake Meyers for an alignment of the Arabidopsis CNL genes, and the USDA Soybean Germplasm Collection for soybean seed  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1104/pp.114.244715">doi:10.1104/pp.114.244715</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25034017">pmid:25034017</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4149710/">pmcid:PMC4149710</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s5vthbedvvffbnrbtlrjtt6tia">fatcat:s5vthbedvvffbnrbtlrjtt6tia</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303060844/http://pdfs.semanticscholar.org/b09e/5d8aeee1c912049cf84427b10807e9c06c43.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b0/9e/b09e5d8aeee1c912049cf84427b10807e9c06c43.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1104/pp.114.244715"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149710" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Structure-based drug discovery using trehalose-6-phosphate phosphatase, an infectious disease target

Megan Cross, University, My, Andreas Hofmann
<span title="2019-05-15">2019</span>
Structure-based sequence analysis of the TPP enzymes of a range of pathogens supported the proposal of three topological groups with structural differences and revealed species-specific variation in what  ...  This work focuses on the TPP enzymes of the parasitic nematodes Toxocara canis and Ancylostoma ceylanicum as the centre of a target-based approach to identify novel TPP inhibitors with potential as early  ...  The structure-based amino acid sequence alignment of nematode TPPs highlights a conserved cysteine residue in the nematode group of mono-enzyme TPPs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.25904/1912/1200">doi:10.25904/1912/1200</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qc3adkch6jggffxj4xzbceyr3e">fatcat:qc3adkch6jggffxj4xzbceyr3e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200724231013/https://research-repository.griffith.edu.au/bitstream/handle/10072/384294/Cross,%20Megan_Final%20Thesis_redacted.pdf;jsessionid=EE15B88B6C300B31D37C73BEC04FDD78?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7a/be/7abe2f4699d5f685f7663d4e389dc037958bae2c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.25904/1912/1200"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

From root tips to phylogenetic branches : a functional and evolutionary study of peroxidases

Filippo Passardi, Claude Penel, Christophe Dunand
<span title="">2006</span>
J'ai ainsi (avec Christophe Dunand) créé une base de données visant à regrouper les séquences de peroxydases et de pouvoir ainsi les comparer de manière rapide et efficace.  ...  Ce travail a fait l'objet de la publication suivante : Passardi F, Longet D, Penel C, Dunand C. The class III peroxidase multigenic family in rice and its evolution in land plants.  ...  (FWF project P18751) to Marcel Zamocky, Christa Jakopitsch and Christian Obinger.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.13097/archive-ouverte/unige:443">doi:10.13097/archive-ouverte/unige:443</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ovmbjsucaza5fgbyhrfwvnp5oq">fatcat:ovmbjsucaza5fgbyhrfwvnp5oq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200422102338/https://archive-ouverte.unige.ch/files/downloads/0/0/0/0/0/4/4/3/unige_443_thesis.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.13097/archive-ouverte/unige:443"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>