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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. The human mineralocorticoid receptor (MR) is one of the main components of the renin-angiotensin-aldosterone system (RAAS), the system that regulates the body exchange of water and sodium. The evolutionary ori...

    Authors: Metaxia Vlassi, Katharina Brauns and Miguel A Andrade-Navarro
    Citation: BMC Structural Biology 2013 13:17
    Content type: Research article Published on:

  2. Persistent organic pollutants (POPs) are persistent in the environment after release from industrial compounds, combustion productions or pesticides. The exposure of POPs has been related to various reproducti...

    Authors: Xian Jin Xu, Ji Guo Su, Anna Rita Bizzarri, Salvatore Cannistraro, Ming Liu, Yi Zeng, Wei Zu Chen and Cun Xin Wang
    Citation: BMC Structural Biology 2013 13:16
    Content type: Research article Published on:

  3. The arginine of the D/E/NRY motif in Rhodopsin family G protein-coupled receptors (GPCRs) is conserved in 96% of these proteins. In some GPCRs, this arginine in transmembrane 3 can form a salt bridge with an a...

    Authors: Margaret M Pruitt, Monica H Lamm and Clark R Coffman
    Citation: BMC Structural Biology 2013 13:15
    Content type: Research article Published on:

  4. Mutation of amino acid sequences in a protein may have diverse effects on its structure and function. Point mutations of even a single amino acid residue in the helices of the non-redundant database may lead t...

    Authors: Nicholus Bhattacharjee and Parbati Biswas
    Citation: BMC Structural Biology 2013 13:9
    Content type: Research article Published on:

  5. The Multidrug Resistance Protein ABCC11/MRP8 is expressed in physiological barriers and tumor breast tissues in which it secretes various substrates including cGMP (cyclic guanosine monophosphate) and 5FdUMP (...

    Authors: Mylène Honorat, Raphaël Terreux, Pierre Falson, Attilio Di Pietro, Charles Dumontet and Lea Payen
    Citation: BMC Structural Biology 2013 13:7
    Content type: Research article Published on:

  6. The post-genomic era poses several challenges. The biggest is the identification of biochemical function for protein sequences and structures resulting from genomic initiatives. Most sequences lack a character...

    Authors: Rajaram Gana, Shruti Rao, Hongzhan Huang, Cathy Wu and Sona Vasudevan
    Citation: BMC Structural Biology 2013 13:6
    Content type: Research article Published on:

  7. To explore novel platinum-based anticancer agents that are distinct from the structure and interaction mode of the traditional cisplatin by forming the bifunctional intrastrand 1,2 GpG adduct, the monofunction...

    Authors: Shanshan Cui, Yan Wang and Guangju Chen
    Citation: BMC Structural Biology 2013 13:4
    Content type: Research article Published on:

  8. The CWxP motif of transmembrane helix 6 (x: any residue) is highly conserved in class A GPCRs. Within this motif, W6.48 is a big star in the theory of the global “toggle switch” because of its key role in the ...

    Authors: Mireia Olivella, Gianluigi Caltabiano and Arnau Cordomí
    Citation: BMC Structural Biology 2013 13:3
    Content type: Research article Published on:

  10. Microsomal CYP2E1 metabolizes about 160 hydrophobic exogens, many of which are environmental pollutants. While metabolising xenobiotics CYP2E1 on one hand facilitates in their excretion and on the other hand a...

    Authors: Volodymyr O Kitam, Oksana V Maksymchuk and Mykola O Chashchyn
    Citation: BMC Structural Biology 2012 12:33
    Content type: Research article Published on:

  11. With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or th...

    Authors: Nicholas Smith, Brandon Campbell, Lin Li, Chuan Li and Emil Alexov
    Citation: BMC Structural Biology 2012 12:31
    Content type: Software Published on:

  12. Toxoplasma gondii is an intracellular coccidian parasite that causes toxoplasmosis. It was estimated that more than one third of the world population is infected by T. gondii, and the disease is critical in fetus...

    Authors: Yap Boon Wooi Tommy, Theam Soon Lim, Rahmah Noordin, Geita Saadatnia and Yee Siew Choong
    Citation: BMC Structural Biology 2012 12:30
    Content type: Research article Published on:

  13. MTMDAT is a program designed to facilitate analysis of mass spectrometry data of proteins and biomolecular complexes that are probed structurally by limited proteolysis. This approach can provide information a...

    Authors: Janosch Hennig, Sjoerd J de Vries, Klaus DM Hennig, Leah Randles, Kylie J Walters, Maria Sunnerhagen and Alexandre MJJ Bonvin
    Citation: BMC Structural Biology 2012 12:29
    Content type: Methodology article Published on:

  14. Interaction of non-structural protein 5A (NS5A) of Hepatitis C virus (HCV) with human kinases namely, casein kinase 1α (ck1α) and protein kinase R (PKR) have different functional implications such as regulatio...

    Authors: Govindarajan Sudha, Subburaj Yamunadevi, Nidhi Tyagi, Saumitra Das and Narayanaswamy Srinivasan
    Citation: BMC Structural Biology 2012 12:28
    Content type: Research article Published on:

  17. P-type ATPases hydrolyze ATP and release energy that is used in the transport of ions against electrochemical gradients across plasma membranes, making these proteins essential for cell viability. Currently, t...

    Authors: Lorena Novoa-Aponte, Andrés León-Torres, Miyer Patiño-Ruiz, Jenifer Cuesta-Bernal, Luz-Mary Salazar, David Landsman, Leonardo Mariño-Ramírez and Carlos-Yesid Soto
    Citation: BMC Structural Biology 2012 12:25
    Content type: Research article Published on:

  18. The inhibition of the activity of β-secretase (BACE-1) is a potentially important approach for the treatment of Alzheimer disease. To explore the mechanism of inhibition, we describe the use of 46 X-ray crysta...

    Authors: Shu Liu, Rao Fu, Xiao Cheng, Sheng-Ping Chen and Li-Hua Zhou
    Citation: BMC Structural Biology 2012 12:21
    Content type: Research article Published on:

  21. Structural genomics approaches, particularly those solving the 3D structures of many proteins with unknown functions, have increased the desire for structure-based function predictions. However, prediction of ...

    Authors: Keisuke Ueno, Katsuhiko Mineta, Kimihito Ito and Toshinori Endo
    Citation: BMC Structural Biology 2012 12:5
    Content type: Research article Published on:

BMC Structural Biology

ISSN: 1472-6807

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