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  3. Sterile alpha motif (Sam) domains are small protein modules that can be involved in homotypic or heterotypic associations and exhibit different functions. Previous studies have demonstrated that the Sam domain...

    Authors: Marilisa Leone, Jason Cellitti and Maurizio Pellecchia

    Citation: BMC Structural Biology 2009 9:59

    Content type: Research article

    Published on:

  4. The functional relevance of many of the recently detected JAK2 mutations, except V617F and exon 12 mutants, in patients with chronic myeloproliferative neoplasia (MPN) has been significantly overlooked. To exp...

    Authors: Tai-Sung Lee, Wanlong Ma, Xi Zhang, Hagop Kantarjian and Maher Albitar

    Citation: BMC Structural Biology 2009 9:58

    Content type: Research article

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  5. Stanniocalcins (STCs) represent small glycoprotein hormones, found in all vertebrates, which have been functionally implicated in Calcium homeostasis. However, recent data from mammalian systems indicated that...

    Authors: Daniel M Trindade, Júlio C Silva, Margareth S Navarro, Iris CL Torriani and Jörg Kobarg

    Citation: BMC Structural Biology 2009 9:57

    Content type: Research article

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  6. The lysosomal 66.3 kDa protein from mouse is a soluble, mannose 6-phosphate containing protein of so far unknown function. It is synthesized as a glycosylated 75 kDa precursor that undergoes limited proteolysi...

    Authors: Kristina Lakomek, Achim Dickmanns, Matthias Kettwig, Henning Urlaub, Ralf Ficner and Torben Lübke

    Citation: BMC Structural Biology 2009 9:56

    Content type: Research article

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  7. The high intracellular salt concentration required to maintain a halophilic lifestyle poses challenges to haloarchaeal proteins that must stay soluble, stable and functional in this extreme environment. Prolif...

    Authors: Jody A Winter, Panayiotis Christofi, Shaun Morroll and Karen A Bunting

    Citation: BMC Structural Biology 2009 9:55

    Content type: Research article

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  9. Bacillus anthracis is the causative agent of anthrax and a potential bioterrorism threat. Here we report the biochemical and structural characterization of B. anthracis (Ames) alanine racemase (Alr ...

    Authors: Rafael M Couñago, Milya Davlieva, Ulrich Strych, Ryan E Hill and Kurt L Krause

    Citation: BMC Structural Biology 2009 9:53

    Content type: Research article

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  11. Estimation of the reliability of specific real value predictions is nontrivial and the efficacy of this is often questionable. It is important to know if you can trust a given prediction and therefore the best...

    Authors: Bent Petersen, Thomas Nordahl Petersen, Pernille Andersen, Morten Nielsen and Claus Lundegaard

    Citation: BMC Structural Biology 2009 9:51

    Content type: Methodology article

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  12. Current protocols yield crystals for <30% of known proteins, indicating that automatically identifying crystallizable proteins may improve high-throughput structural genomics efforts. We introduce CRYSTALP2, a...

    Authors: Lukasz Kurgan, Ali A Razib, Sara Aghakhani, Scott Dick, Marcin Mizianty and Samad Jahandideh

    Citation: BMC Structural Biology 2009 9:50

    Content type: Methodology article

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  13. Conformational flexibility in structured RNA frequently is critical to function. The 30S ribosomal subunit exists in different conformations in different functional states due to changes in the central part of...

    Authors: Wayne Huggins, Sujit K Ghosh and Paul Wollenzien

    Citation: BMC Structural Biology 2009 9:49

    Content type: Research article

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  14. The E1 protein of Hepatitis C Virus (HCV) can be dissected into two distinct hydrophobic regions: a central domain containing an hypothetical fusion peptide (FP), and a C-terminal domain (CT) comprising two se...

    Authors: Roberto Bruni, Angela Costantino, Elena Tritarelli, Cinzia Marcantonio, Massimo Ciccozzi, Maria Rapicetta, Gamal El Sawaf, Alessandro Giuliani and Anna Rita Ciccaglione

    Citation: BMC Structural Biology 2009 9:48

    Content type: Research article

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  16. The Asp-box is a short sequence and structure motif that folds as a well-defined β-hairpin. It is present in different folds, but occurs most prominently as repeats in β-propellers. Asp-box β-propellers are kn...

    Authors: Esben M Quistgaard and Søren S Thirup

    Citation: BMC Structural Biology 2009 9:46

    Content type: Research article

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  17. It is increasingly recognized that protein functions often require intricate conformational dynamics, which involves a network of key amino acid residues that couple spatially separated functional sites. Treme...

    Authors: Wenjun Zheng and Mustafa Tekpinar

    Citation: BMC Structural Biology 2009 9:45

    Content type: Research article

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  18. Amyloidoses are a group of usually fatal diseases, probably caused by protein misfolding and subsequent aggregation into amyloid fibrillar deposits. The mechanisms involved in amyloid fibril formation are larg...

    Authors: Kimon K Frousios, Vassiliki A Iconomidou, Carolina-Maria Karletidi and Stavros J Hamodrakas

    Citation: BMC Structural Biology 2009 9:44

    Content type: Research article

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  19. Notch signaling drives developmental processes in all metazoans. The receptor binding region of the human Notch ligand Jagged-1 is made of a DSL (Delta/Serrate/Lag-2) domain and two atypical epidermal growth f...

    Authors: Alessandro Pintar, Corrado Guarnaccia, Somdutta Dhir and Sándor Pongor

    Citation: BMC Structural Biology 2009 9:43

    Content type: Research article

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  21. Methods that can automatically assess the quality of computationally predicted protein structures are important, as they enable the selection of the most accurate structure from an ensemble of predictions. Ass...

    Authors: Kevin W DeRonne and George Karypis

    Citation: BMC Structural Biology 2009 9:41

    Content type: Research article

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  22. The Actinobacteria phylum represents one of the largest and most diverse groups of bacteria, encompassing many important and well-characterized organisms including Streptomyces, Bifidobacterium, Corynebacterium a...

    Authors: Beile Gao, Seiji Sugiman-Marangos, Murray S Junop and Radhey S Gupta

    Citation: BMC Structural Biology 2009 9:40

    Content type: Research article

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  23. Previously, ways to adapt docking programs that were developed for modelling inhibitor-receptor interaction have been explored. Two main issues were discussed. First, when trying to model catalysis a reaction ...

    Authors: P Benjamin Juhl, Peter Trodler, Sadhna Tyagi and Jürgen Pleiss

    Citation: BMC Structural Biology 2009 9:39

    Content type: Research article

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  25. The hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. The fold appears to have a strong association with fatty acid biosynthesis, its regulatio...

    Authors: Lakshmi S Pidugu, Koustav Maity, Karthikeyan Ramaswamy, Namita Surolia and Kaza Suguna

    Citation: BMC Structural Biology 2009 9:37

    Content type: Research article

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  26. The Dbl-family of guanine nucleotide exchange factors (GEFs) activate the cytosolic GTPases of the Rho family by enhancing the rate of exchange of GTP for GDP on the cognate GTPase. This catalytic activity res...

    Authors: Meiying Zheng, Tomasz Cierpicki, Ko Momotani, Mykhaylo V Artamonov, Urszula Derewenda, John H Bushweller, Avril V Somlyo and Zygmunt S Derewenda

    Citation: BMC Structural Biology 2009 9:36

    Content type: Research article

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  27. The selection of the most accurate protein model from a set of alternatives is a crucial step in protein structure prediction both in template-based and ab initio approaches. Scoring functions have been developed...

    Authors: Pascal Benkert, Torsten Schwede and Silvio CE Tosatto

    Citation: BMC Structural Biology 2009 9:35

    Content type: Research article

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  28. Several studies have demonstrated that protein fold space is structured hierarchically and that power-law statistics are satisfied in relation between the numbers of protein families and protein folds (or supe...

    Authors: Jun-ichi Ito, Yuki Sonobe, Kazuyoshi Ikeda, Kentaro Tomii and Junichi Higo

    Citation: BMC Structural Biology 2009 9:34

    Content type: Research article

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  29. The identification of protein domains plays an important role in protein structure comparison. Domain query size and composition are critical to structure similarity search algorithms such as the Vector Alignm...

    Authors: Kenneth Evan Thompson, Yanli Wang, Tom Madej and Stephen H Bryant

    Citation: BMC Structural Biology 2009 9:33

    Content type: Research article

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  30. Defects in the human Shwachman-Bodian-Diamond syndrome (SBDS) protein-coding gene lead to the autosomal recessive disorder characterised by bone marrow dysfunction, exocrine pancreatic insufficiency and skelet...

    Authors: C Leong Ng, David G Waterman, Eugene V Koonin, Alison D Walters, James PJ Chong, Michail N Isupov, Andrey A Lebedev, David HJ Bunka, Peter G Stockley, Miguel Ortiz-Lombardía and Alfred A Antson

    Citation: BMC Structural Biology 2009 9:32

    Content type: Research article

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  31. Recently, perfluorooctanoic acid (PFOA) has become a significant issue in many aspects of environmental ecology, toxicology, pathology and life sciences because it may have serious effects on the endocrine, im...

    Authors: Ling-Ling Wu, Hong-Wen Gao, Nai-Yun Gao, Fang-Fang Chen and Ling Chen

    Citation: BMC Structural Biology 2009 9:31

    Content type: Research article

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  32. DNA recognition by proteins is one of the most important processes in living systems. Therefore, understanding the recognition process in general, and identifying mutual recognition sites in proteins and DNA i...

    Authors: Munazah Andrabi, Kenji Mizuguchi, Akinori Sarai and Shandar Ahmad

    Citation: BMC Structural Biology 2009 9:30

    Content type: Research article

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  35. Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from s...

    Authors: Adrien Saladin, Sébastien Fiorucci, Pierre Poulain, Chantal Prévost and Martin Zacharias

    Citation: BMC Structural Biology 2009 9:27

    Content type: Software

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  36. In addition to structural domains, most eukaryotic proteins possess intrinsically disordered (ID) regions. Although ID regions often play important functional roles, their accurate identification is difficult....

    Authors: Satoshi Fukuchi, Keiichi Homma, Yoshiaki Minezaki, Takashi Gojobori and Ken Nishikawa

    Citation: BMC Structural Biology 2009 9:26

    Content type: Research article

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  37. Solvent accessibility (ASA) of amino acid residues is often transformed from absolute values of exposed surface area to their normalized relative values. This normalization is typically attained by assuming a hig...

    Authors: Hemajit Singh and Shandar Ahmad

    Citation: BMC Structural Biology 2009 9:25

    Content type: Research article

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  38. An important question of biological relevance is the polymorphism of the double-helical DNA structure in its free form, and the changes that it undergoes upon protein-binding. We have analysed a database of fr...

    Authors: Arvind Marathe, Deepti Karandur and Manju Bansal

    Citation: BMC Structural Biology 2009 9:24

    Content type: Research article

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  40. The correlated mutations concept is based on the assumption that interacting protein residues coevolve, so that a mutation in one of the interacting counterparts is compensated by a mutation in the other. Appr...

    Authors: Sergey A Samsonov, Joan Teyra, Gerd Anders and M Teresa Pisabarro

    Citation: BMC Structural Biology 2009 9:22

    Content type: Research article

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  41. Epidemics caused by highly pathogenic avian influenza virus (HPAIV) are a continuing threat to human health and to the world's economy. The development of approaches, which help to understand the significance ...

    Authors: Veljko Veljkovic, Nevena Veljkovic, Claude P Muller, Sybille Müller, Sanja Glisic, Vladimir Perovic and Heinz Köhler

    Citation: BMC Structural Biology 2009 9:21

    Content type: Research article

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  43. Cartoon-style illustrative renderings of proteins can help clarify structural features that are obscured by space filling or balls and sticks style models, and recent advances in programmable graphics cards of...

    Authors: Joseph R Weber

    Citation: BMC Structural Biology 2009 9:19

    Content type: Software

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  44. The transmission electron microscope is used to acquire structural information of macromolecular complexes. However, as any other imaging device, it introduces optical aberrations that must be corrected if hig...

    Authors: Carlos Oscar S Sorzano, Abraham Otero, Estefanía M Olmos and José María Carazo

    Citation: BMC Structural Biology 2009 9:18

    Content type: Methodology article

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  45. Staphylococcus aureus is a Gram-positive pathogenic bacterium causing many kinds of infections from mild respiratory tract infections to life-threatening states as sepsis. Recent emergence of S. aureus strains re...

    Authors: Outi Heikkinen, Raili Seppala, Helena Tossavainen, Sami Heikkinen, Harri Koskela, Perttu Permi and Ilkka Kilpeläinen

    Citation: BMC Structural Biology 2009 9:17

    Content type: Research article

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  46. Structure-based drug design (SBDD) can provide valuable guidance to drug discovery programs. Robust construct design and expression, protein purification and characterization, protein crystallization, and high...

    Authors: Maria A Argiriadi, Silvino Sousa, David Banach, Douglas Marcotte, Tao Xiang, Medha J Tomlinson, Megan Demers, Christopher Harris, Silvia Kwak, Jennifer Hardman, Margaret Pietras, Lisa Quinn, Jennifer DiMauro, Baofu Ni, John Mankovich, David W Borhani…

    Citation: BMC Structural Biology 2009 9:16

    Content type: Research article

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  47. Nonribosomal peptides (NRPs), bioactive secondary metabolites produced by many microorganisms, show a broad range of important biological activities (e.g. antibiotics, immunosuppressants, antitumor agents). NR...

    Authors: Ségolène Caboche, Maude Pupin, Valérie Leclère, Phillipe Jacques and Gregory Kucherov

    Citation: BMC Structural Biology 2009 9:15

    Content type: Methodology article

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  48. Uridine phosphorylase (UPP) is a key enzyme of pyrimidine salvage pathways, catalyzing the reversible phosphorolysis of ribosides of uracil to nucleobases and ribose 1-phosphate. It is also a critical enzyme i...

    Authors: Tarmo P Roosild, Samantha Castronovo, Michael Fabbiani and Giuseppe Pizzorno

    Citation: BMC Structural Biology 2009 9:14

    Content type: Research article

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  49. Conformational change induced by the binding of a substrate or coenzyme is a poorly understood stage in the process of enzyme catalysed reactions. For enzymes that exhibit a domain movement, the conformational...

    Authors: Guoying Qi and Steven Hayward

    Citation: BMC Structural Biology 2009 9:13

    Content type: Database

    Published on:

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ISSN: 1472-6807

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