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BMC Structural Biology

Computational analysis

Section edited by David Burke

This section incorporates all aspects of the methods, applications and analysis of the structure of biological macromolecules incorporating substantial analysis using computational methods.

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  1. Content type: Research Article

    Membrane proteins are difficult targets for structure prediction due to the limited structural data deposited in Protein Data Bank. Most computational methods for membrane protein structure prediction are base...

    Authors: Dorota Latek

    Citation: BMC Structural Biology 2017 17:8

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  2. Content type: Research Article

    The bHLH transcription factor TWIST1 plays a key role in the embryonic development and in tumorigenesis. Some loss-of-function mutations of the TWIST1 gene have been shown to cause an autosomal dominant craniosyn...

    Authors: Charlotte Bouard, Raphael Terreux, Agnès Tissier, Laurent Jacqueroud, Arnaud Vigneron, Stéphane Ansieau, Alain Puisieux and Léa Payen

    Citation: BMC Structural Biology 2017 17:6

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  3. Content type: Research Article

    Formamidopyrimidine-DNA glycosylase (Fpg) removes abundant pre-mutagenic 8-oxoguanine (oxoG) bases from DNA through nucleophilic attack of its N-terminal proline at C1′ of the damaged nucleotide. Since oxoG ef...

    Authors: Alexander V. Popov, Anton V. Endutkin, Yuri N. Vorobjev and Dmitry O. Zharkov

    Citation: BMC Structural Biology 2017 17:5

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  4. Content type: Research Article

    The Spumaretrovirinae (foamy viruses) and the Orthoretrovirinae (e.g. HIV) share many similarities both in genome structure and the sequences of the core viral encoded proteins, such as the aspartyl protease and ...

    Authors: William R. Taylor, Jonathan P. Stoye and Ian A. Taylor

    Citation: BMC Structural Biology 2017 17:3

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  5. Content type: Research article

    TPX2 (Targeting Protein for Xklp2) is essential for spindle assembly, activation of the mitotic kinase Aurora A and for triggering microtubule nucleation. Homologs of TPX2 in Chordata and plants were previousl...

    Authors: Luis Sanchez-Pulido, Laurent Perez, Steffen Kuhn, Isabelle Vernos and Miguel A. Andrade-Navarro

    Citation: BMC Structural Biology 2016 16:17

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  6. Content type: Research article

    The Plasmodium falciparum M18 Aspartyl Aminopeptidase (PfM18AAP) is only aspartyl aminopeptidase which is found in the genome of P. falciparum and is essential for its survival. The PfM18AAP enzyme performs vario...

    Authors: Madhulata Kumari, Subhash Chandra, Neeraj Tiwari and Naidu Subbarao

    Citation: BMC Structural Biology 2016 16:12

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  7. Content type: Research article

    We comprehensively analyzed X-ray cocrystal structures of dipeptidyl peptidase IV (DPP-4) and its inhibitor to clarify whether DPP-4 alters its general or partial structure according to the inhibitor used and ...

    Authors: Hiroyuki Nojima, Kazuhiko Kanou, Genki Terashi, Mayuko Takeda-Shitaka, Gaku Inoue, Koichiro Atsuda, Chihiro Itoh, Chie Iguchi and Hajime Matsubara

    Citation: BMC Structural Biology 2016 16:11

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  8. Content type: Research article

    This study investigates the allosteric coupling that exists between the intra- and extracellular parts of human β2-adrenergic receptor (β2-AR), in the presence of the intracellular loop 3 (ICL3), which is missing...

    Authors: Canan Ozgur, Pemra Doruker and E. Demet Akten

    Citation: BMC Structural Biology 2016 16:9

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  9. Content type: Research article

    During inflammation, leukocytes are captured by the selectin family of adhesion receptors lining blood vessels to facilitate exit from the bloodstream. E-selectin is upregulated on stimulated endothelial cells...

    Authors: Anne D. Rocheleau, Thong M. Cao, Tait Takitani and Michael R. King

    Citation: BMC Structural Biology 2016 16:10

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  10. Content type: Software

    The term ‘molecular cartography’ encompasses a family of computational methods for two-dimensional transformation of protein structures and analysis of their physicochemical properties. The underlying algorith...

    Authors: Dimitrios Georgios Kontopoulos, Dimitrios Vlachakis, Georgia Tsiliki and Sofia Kossida

    Citation: BMC Structural Biology 2016 16:4

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    The Publisher's Erratum to this article has been published in BMC Structural Biology 2016 16:6

  11. Content type: Research article

    Protein-protein interactions (PPIs) mediate the vast majority of biological processes, therefore, significant efforts have been directed to investigate PPIs to fully comprehend cellular functions. Predicting c...

    Authors: Surabhi Maheshwari and Michal Brylinski

    Citation: BMC Structural Biology 2015 15:23

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  12. Content type: Research article

    Many β-strands are not flat but bend and/or twist. However, although almost all β-strands have a twist, not all have a bend, suggesting that the underlying force(s) driving β-strand bending is distinct from th...

    Authors: Kazuo Fujiwara, Shinichi Ebisawa, Yuka Watanabe, Hiromi Fujiwara and Masamichi Ikeguchi

    Citation: BMC Structural Biology 2015 15:21

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  13. Content type: Research article

    RNA ligases 2 are scarce and scattered across the tree of life. Two members of this family are well studied: the mitochondrial RNA editing ligase from the parasitic trypanosomes (Kinetoplastea), a promising dr...

    Authors: Sandrine Moreira, Emmanuel Noutahi, Guillaume Lamoureux and Gertraud Burger

    Citation: BMC Structural Biology 2015 15:20

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  14. Content type: Research article

    Helicobacter pylori is an important factor in the development of diseases such as ulcer and gastric cancer. This bacterium uses a periplasmic transporter, UreI, to deliver urea to the ...

    Authors: Javier Cáceres-Delpiano, Jaime Teneb, Rodrigo Mansilla, Apolinaria García and Alexis Salas-Burgos

    Citation: BMC Structural Biology 2015 15:11

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  15. Content type: Research Article

    Thanks to the growth in sequence and structure databases, more than 50 million sequences are now available in UniProt and 100,000 structures in the PDB. Rich information about protein-protein interfaces can be...

    Authors: Kumaran Baskaran, Jose M Duarte, Nikhil Biyani, Spencer Bliven and Guido Capitani

    Citation: BMC Structural Biology 2014 14:22

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