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Virtual Screening of potential drug-like inhibitors against Lysine/DAP pathway of Mycobacterium tuberculosis

Aarti Garg, Rupinder Tewari, Gajendra PS Raghava
2010 BMC Bioinformatics  
Conclusion: The above-mentioned virtual screening procedures helped in the identification of several potent candidates that possess inhibitory activity against Mtb DHDPS.  ...  Therefore, these novel scaffolds/candidates which could have the potential to inhibit Mtb DHDPS enzyme would represent promising starting points as lead compounds and certainly aid the experimental designing  ...  This article has been published as part of BMC Bioinformatics Volume 11 Supplement 1, 2010: Selected articles from the Eighth Asia-Pacific Bioinformatics Conference (APBC 2010).  ... 
doi:10.1186/1471-2105-11-s1-s53 pmid:20122228 pmcid:PMC3009526 fatcat:sctfr7fggrb2bfc5b654t3yc5m

Rational Design of DNA Nanoarchitectures

Udo Feldkamp, Christof M. Niemeyer
2006 Angewandte Chemie International Edition  
We thank Kersten Rabe for help with the artwork of the frontispiece.  ...  " of the University of Dortmund.  ...  superstructures.  ... 
doi:10.1002/anie.200502358 pmid:16470892 fatcat:ebotbu2ct5bxbg4puwszeraojy

Blind Test of Physics-Based Prediction of Protein Structures

M. Scott Shell, S. Banu Ozkan, Vincent Voelz, Guohong Albert Wu, Ken A. Dill
2009 Biophysical Journal  
Because these predictions have about the same level of accuracy as typical bioinformatics methods, and do not utilize information from databases of known native structures, this work opens up the possibility  ...  Coarse conformational sampling is performed using the zipping and assembly method (ZAM), an approach that is designed to mimic the putative physical routes of protein folding.  ...  We appreciate the use of the computing resources provided by the NCSA Supercomputing Center in Illinois, and the UCSF QB3 computing cluster provided by Andrej Sali and his group.  ... 
doi:10.1016/j.bpj.2008.11.009 pmid:19186130 pmcid:PMC2716649 fatcat:thj6xkyiyvfitcrrsf6uyibih4

P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure

Radoslav Krivák, David Hoksza
2018 Journal of Cheminformatics  
Conclusions: P2Rank is a new open source software package for ligand binding site prediction from protein structure.  ...  P2Rank has a lightweight installation and does not depend on other bioinformatics tools or large structural or sequence databases.  ...  Every relevant ligand contributes with equal weight toward the final success rate.  ... 
doi:10.1186/s13321-018-0285-8 pmid:30109435 fatcat:w6kiu2kl5rar3nyqpbx5l2mrey

Global data for local science: Assessing the scale of data infrastructures in biological and biomedical research

Sabina Leonelli
2013 BioSocieties  
Grid.  ...  At the same time, databases are not deemed successful unless they facilitate the re-use of data towards new scientific discoveries, which often involves engaging with several highly diverse and inherently  ...  To support generalizability of the findings, it is necessary to enlarge the population by increasing the number of participants from the chosen institution and/or to include other academic institutions  ... 
doi:10.1057/biosoc.2013.23 fatcat:oatnrcvej5hlll3knpd7tlpkdu

Coiled-coil oligomerization controls localization of the plasma membrane REMORINs

Denis Martinez, Anthony Legrand, Julien Gronnier, Marion Decossas, Paul Gouguet, Olivier Lambert, Mélanie Berbon, Loris Verron, Axelle Grélard, Veronique Germain, Antoine Loquet, Sébastien Mongrand (+1 others)
2018 Journal of Structural Biology  
REMORINs are nanodomain-organized proteins located in the plasma membrane  ...  Acknowledgments We acknowledge the financial support by the ANR (ANR-13-PDOC-0017-01 to B.H. and ANR-14-CE09-0020-01 to A.L.), the IdEx Bordeaux "Investments for the  ...  We have here taken advantage of several biochemical, biophysical and bioinformatic tools to decipher the role and the structure of REMORINs' assembly.  ... 
doi:10.1016/j.jsb.2018.02.003 pmid:29481850 fatcat:q5vf5rzwe5cgdizr5e6m46ghoi

Practical application of bioinformatics by the multidisciplinary VIZIER consortium

Alexander E. Gorbalenya, Philippe Lieutaud, Mark R. Harris, Bruno Coutard, Bruno Canard, Gerard J. Kleywegt, Alexander A. Kravchenko, Dmitry V. Samborskiy, Igor A. Sidorov, Andrey M. Leontovich, T. Alwyn Jones
2010 Antiviral Research  
From the management of the information flow of the project, to bioinformatics-mediated selection of RNA viruses and prediction of protein targets, to the analysis of 3D protein structures and antiviral  ...  This review focuses on bioinformatics technologies employed by the EU-sponsored multidisciplinary VIZIER consortium (Comparative Structural Genomics of Viral Enzymes Involved in Replication, FP6 PROJECT  ...  The Viralis development and usage were also partially supported by grants from the Netherlands Bioinformatics Center (BioRangeSP3.2.2) and the Collaborative Agreement in Bioinformatics between LUMC and  ... 
doi:10.1016/j.antiviral.2010.02.005 pmid:20153379 pmcid:PMC7172516 fatcat:hpnoegkpjzgkbjqy6r6oxl77ga

A survey of protein interaction data and multigenic inherited disorders

Antonio Mora, Katerina Michalickova, Ian M Donaldson
2013 BMC Bioinformatics  
The accompanying R script can be used to reproduce the work and track progress in this area as databases change.  ...  A further 68 disease overlaps were found only in the KEGG pathway database. No single database contained all significant overlaps thus stressing the importance of data integration.  ...  Acknowledgments The authors would like to thank Sabry Razick and Paul Boddie for their support with the iRefIndex database. We also thank George Magklaras of EMBNet Norway for technical support.  ... 
doi:10.1186/1471-2105-14-47 pmid:23398688 pmcid:PMC3598893 fatcat:setd53qtz5bhrd6rh4plwskygm

Efficient production of chimeric Human papillomavirus 16 L1 protein bearing the M2e influenza epitope in Nicotiana benthamiana plants

Slavica Matić, Riccardo Rinaldi, Vera Masenga, Emanuela Noris
2011 BMC Biotechnology  
Conclusions: In this study, we report for the first time the transient expression and the self-assembly of a chimeric HPV-16 L1 bearing the M2e influenza epitope in plants, representing also the first  ...  Results: We investigated the potential of HPV-16 L1 to act as a carrier of two foreign epitopes from Influenza A virus: (i) M2e 2-24 , ectodomain of the M2 protein (M2e), that is highly conserved among  ...  Acknowledgements The authors wish to thank the late Dr. R.G. Milne, to whose memory this paper is dedicated, for his contribution in the electron-microscopy work. We also wish to thank Prof. E.P.  ... 
doi:10.1186/1472-6750-11-106 pmid:22085463 pmcid:PMC3248878 fatcat:ibmfh37ovfctpla527utkiwmo4

Pepsin Digest of Gliadin Forms Spontaneously Amyloid‐Like Nanostructures Influencing the Expression of Selected Pro‐Inflammatory, Chemoattractant, and Apoptotic Genes in Caco‐2 Cells: Implications for Gluten‐Related Disorders

Maria Georgina Herrera, Francesco Nicoletti, Marion Gras, Philipp W. Dörfler, Nicolo Tonali, Yvonne Hannappel, Inga Ennen, Andreas Hütten, Thomas Hellweg, Karen M. Lammers, Veronica I. Dodero
2021 Molecular Nutrition & Food Research  
The self-assembly of p-gliadin starts at a concentration of 0.40 μg/ml.  ...  This work demonstrates that p-gliadin is interfacial active, forming spontaneously amyloid-type structures that trigger genes in the Caco-2 cell line involved in the recruitment of specialized immune cells  ...  Acknowledgements This work was initially funded by the Alexander von Humboldt Foundation  ... 
doi:10.1002/mnfr.202100200 pmid:34110092 fatcat:43ygot2ddvbndbrzyb3ykdg374

Structural Analysis of Influenza A Virus Matrix Protein M1 and Its Self-Assemblies at Low pH

Eleonora V. Shtykova, Lyudmila A. Baratova, Natalia V. Fedorova, Victor A. Radyukhin, Alexander L. Ksenofontov, Vladimir V. Volkov, Alexander V. Shishkov, Alexey A. Dolgov, Liudmila A. Shilova, Oleg V. Batishchev, Cy M. Jeffries, Dmitri I. Svergun (+1 others)
2013 PLoS ONE  
The absence of high-resolution data on the full-length M1 makes the structural investigation of the intact protein particularly important.  ...  The NM-domain does not spontaneously self assemble supporting the key role of the C-terminus of M1 in the formation of supramolecular structures.  ...  Magretova for the excellent technical assistance. Author Contributions  ... 
doi:10.1371/journal.pone.0082431 pmid:24358182 pmcid:PMC3865061 fatcat:s5khghl5kzdglftd6jrxn7lp7a

Nano on reflection

2016 Nature Nanotechnology  
reflection A number of experts from different areas of nanotechnology describe how the field has evolved in the last ten years.  ...  Bursten is a philosopher, blogger and writer based in the Department of Philosophy, University of Kentucky, USA.  ...  The widespread integration of renewable, intermittent energy sources (wind, solar) is dependent on developing efficient low-cost energy storage for load-levelling the electric grid.  ... 
doi:10.1038/nnano.2016.232 pmid:27703248 fatcat:fotj5wfcgrg5da6akiuit5bbee

Digital Capitalism and Critical Media Education

Horst Niesyto
2021 Seminar.net  
The third part discusses the manoeuvres of the IT industry in Germany to gain more influence on the education sector.  ...  Against the background of these developments, the last part outlines the need for alternative pathways and presents dimensions of a critical media education.[1] [1] The article is based on two German language  ...  It can be assumed that bioinformatics in particular will be heavily courted by various commercial enterprises in the future in order to open up new markets through the use of corresponding technologies  ... 
doi:10.7577/seminar.4224 fatcat:i67wada7kzhfzch47tgjygafee

The Y. bercovieri Anbu crystal structure sheds light on the evolution of highly (pseudo)symmetric multimers

Anna Piasecka, Honorata Czapinska, Marie-Theres Vielberg, Roman H. Szczepanowski, Reiner Kiefersauer, Simon Reed, Michael Groll, Matthias Bochtler
2018 Journal of Molecular Biology  
The crystal structure reveals that YbAnbu subunits form tight dimers, held together in part by the Anbu specific C-terminal helices.  ...  However, we could document orthophosphate production from ATP catalyzed by the ATP-grasp protein encoded in the Y. bercovieri Anbu operon.  ...  Robert Huber on the occasion of his 80th birthday.  ... 
doi:10.1016/j.jmb.2017.11.016 pmid:29258816 pmcid:PMC6376114 fatcat:zt7lkwep5zb2rg2iryef5t4t64

A folded conformation of MukBEF and Cohesin [article]

Frank Buermann, Byung-Gil Lee, Thane Than, Ludwig Sinn, Francis J O'Reilly, Stanislau Yatskevich, Juri Rappsilber, Bin Hu, Kim Nasmyth, Jan Lowe
2018 bioRxiv   pre-print
Bending at the elbow brings into proximity the hinge dimerization domain and the head/kleisin module, situated at opposite ends of the arms.  ...  We show that both contain a dynamic coiled-coil discontinuity, the elbow, near the middle of their arms that permits a folded conformation.  ...  caused by the grid preparation procedure.  ... 
doi:10.1101/464701 fatcat:zpceghzznfhszpr7kc34wsxxvy
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