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  1. The transient, or permanent, association of proteins to form organized complexes is one of the most common mechanisms of regulation of biological processes. Systematic physico-chemical studies of the binding i...

    Authors: Andrea Zen, Cristian Micheletti, Ozlem Keskin and Ruth Nussinov
    Citation: BMC Structural Biology 2010 10:26
  2. ALG-2 (a gene product of PDCD6) belongs to the penta-EF-hand (PEF) protein family and Ca2+-dependently interacts with various intracellular proteins including mammalian Alix, an adaptor protein in the ESCRT syste...

    Authors: Tatsutoshi Inuzuka, Hironori Suzuki, Masato Kawasaki, Hideki Shibata, Soichi Wakatsuki and Masatoshi Maki
    Citation: BMC Structural Biology 2010 10:25
  3. Aromatic amino acids play a critical role in protein-glycan interactions. Clusters of surface aromatic residues and their features may therefore be useful in distinguishing glycan-binding sites as well as pred...

    Authors: Andrew C Doxey, Zhenyu Cheng, Barbara A Moffatt and Brendan J McConkey
    Citation: BMC Structural Biology 2010 10:23
  4. Accurate protein loop structure models are important to understand functions of many proteins. Identifying the native or near-native models by distinguishing them from the misfolded ones is a critical step in ...

    Authors: Yaohang Li, Ionel Rata, See-wing Chiu and Eric Jakobsson
    Citation: BMC Structural Biology 2010 10:22
  5. Type III secretion systems are a common virulence mechanism in many Gram-negative bacterial pathogens. These systems use a nanomachine resembling a molecular needle and syringe to provide an energized conduit ...

    Authors: Michael L Barta, Lingling Zhang, Wendy L Picking and Brian V Geisbrecht
    Citation: BMC Structural Biology 2010 10:21
  6. Structural flexibility is an important characteristic of proteins because it is often associated with their function. The movement of a polypeptide segment in a protein can be broken down into two types of mot...

    Authors: Shuichi Hirose, Kiyonobu Yokota, Yutaka Kuroda, Hiroshi Wako, Shigeru Endo, Satoru Kanai and Tamotsu Noguchi
    Citation: BMC Structural Biology 2010 10:20
  7. Kinesin motors hydrolyze ATP to produce force and move along microtubules, converting chemical energy into work by a mechanism that is only poorly understood. Key transitions and intermediate states in the pro...

    Authors: Elisabeth Heuston, C Eric Bronner, F Jon Kull and Sharyn A Endow
    Citation: BMC Structural Biology 2010 10:19
  8. Topological descriptors, other graph measures, and in a broader sense, graph-theoretical methods, have been proven as powerful tools to perform biological network analysis. However, the majority of the develop...

    Authors: Matthias M Dehmer, Nicola N Barbarini, Kurt K Varmuza and Armin A Graber
    Citation: BMC Structural Biology 2010 10:18
  9. Dengue virus along with the other members of the flaviviridae family has reemerged as deadly human pathogens. Understanding the mechanistic details of these infections can be highly rewarding in developing eff...

    Authors: Rupali A Gadkari and Narayanaswamy Srinivasan
    Citation: BMC Structural Biology 2010 10:17
  10. The unique S28 family of proteases is comprised of the carboxypeptidase PRCP and the aminopeptidase DPP7. The structural basis of the different substrate specificities of the two enzymes is not understood nor ...

    Authors: Stephen M Soisson, Sangita B Patel, Pravien D Abeywickrema, Noel J Byrne, Ronald E Diehl, Dawn L Hall, Rachael E Ford, John C Reid, Keith W Rickert, Jennifer M Shipman, Sujata Sharma and Kevin J Lumb
    Citation: BMC Structural Biology 2010 10:16
  11. The adaptor protein RACK1 (receptor of activated kinase 1) was originally identified as an anchoring protein for protein kinase C. RACK1 is a 36 kDa protein, and is composed of seven WD repeats which mediate i...

    Authors: Kaliandra A Gonçalves, Julio C Borges, Julio C Silva, Priscila F Papa, Gustavo C Bressan, Iris L Torriani and Jörg Kobarg
    Citation: BMC Structural Biology 2010 10:15
  12. Pyrimidine-preferring N-ribohydrolases (CU-NHs) are a class of Ca2+-dependent enzymes that catalyze the hydrolytic cleavage of the N-glycosidic bond in pyrimidine nucleosides. With the exception of few selected o...

    Authors: Gianpiero Garau, Laura Muzzolini, Paola Tornaghi and Massimo Degano
    Citation: BMC Structural Biology 2010 10:14
  13. Zhx 1 to 3 (zinc-fingers and homeoboxes) form a set of paralogous genes encoding multi-domain proteins. ZHX proteins consist of two zinc fingers followed by five homeodomains. ZHXs have biological roles in cell c...

    Authors: Louise E Bird, Jingshan Ren, Joanne E Nettleship, Gert E Folkers, Raymond J Owens and David K Stammers
    Citation: BMC Structural Biology 2010 10:13
  14. Progesterone binding to the surface of the amphibian oocyte initiates the meiotic divisions. Our previous studies with Rana pipiens oocytes indicate that progesterone binds to a plasma membrane site within the ex...

    Authors: Gene A Morrill, Adele B Kostellow and Amir Askari
    Citation: BMC Structural Biology 2010 10:12
  15. Survival of the human pathogen, Neisseria meningitidis, requires an effective response to oxidative stress resulting from the release of hydrogen peroxide by cells of the human immune system. In N. meningitidis, ...

    Authors: Sarah Sainsbury, Jingshan Ren, Joanne E Nettleship, Nigel J Saunders, David I Stuart and Raymond J Owens
    Citation: BMC Structural Biology 2010 10:10
  16. A protein structure can be determined by solving a so-called distance geometry problem whenever a set of inter-atomic distances is available and sufficient. However, the problem is intractable in general and h...

    Authors: Robert T Davis, Claus Ernst and Di Wu
    Citation: BMC Structural Biology 2010 10(Suppl 1):S7

    This article is part of a Supplement: Volume 10 Supplement 1

  17. Predicting B-cell epitopes is very important for designing vaccines and drugs to fight against the infectious agents. However, due to the high complexity of this problem, previous prediction methods that focus...

    Authors: Liang Zhao and Jinyan Li
    Citation: BMC Structural Biology 2010 10(Suppl 1):S6

    This article is part of a Supplement: Volume 10 Supplement 1

  18. Currently a huge amount of protein-protein interaction data is available from high throughput experimental methods. In a large network of protein-protein interactions, groups of proteins can be identified as f...

    Authors: Ataur R Katebi, Andrzej Kloczkowski and Robert L Jernigan
    Citation: BMC Structural Biology 2010 10(Suppl 1):S4

    This article is part of a Supplement: Volume 10 Supplement 1

  19. In the last decade, various coarse-grained elastic network models have been developed to study the large-scale motions of proteins and protein complexes where computer simulations using detailed all-atom model...

    Authors: Tu-Liang Lin and Guang Song
    Citation: BMC Structural Biology 2010 10(Suppl 1):S3

    This article is part of a Supplement: Volume 10 Supplement 1

  20. Prediction of long-range inter-residue contacts is an important topic in bioinformatics research. It is helpful for determining protein structures, understanding protein foldings, and therefore advancing the a...

    Authors: Peng Chen and Jinyan Li
    Citation: BMC Structural Biology 2010 10(Suppl 1):S2

    This article is part of a Supplement: Volume 10 Supplement 1

  21. Many proteins undergo extensive conformational changes as part of their functionality. Tracing these changes is important for understanding the way these proteins function. Traditional biophysics-based conform...

    Authors: Nurit Haspel, Mark Moll, Matthew L Baker, Wah Chiu and Lydia E Kavraki
    Citation: BMC Structural Biology 2010 10(Suppl 1):S1

    This article is part of a Supplement: Volume 10 Supplement 1

  22. With the classical, active-site oriented drug-development approach reaching its limits, protein ligand-binding sites in general and allosteric sites in particular are increasingly attracting the interest of me...

    Authors: Alejandro Panjkovich and Xavier Daura
    Citation: BMC Structural Biology 2010 10:9
  23. GPR17 is a hybrid G-protein-coupled receptor (GPCR) activated by two unrelated ligand families, extracellular nucleotides and cysteinyl-leukotrienes (cysteinyl-LTs), and involved in brain damage and repair. It...

    Authors: Chiara Parravicini, Maria P Abbracchio, Piercarlo Fantucci and Graziella Ranghino
    Citation: BMC Structural Biology 2010 10:8
  24. Human blood coagulation factor VIII (fVIII) is a large plasma glycoprotein with sequential domain arrangement in the order A1-a1-A2-a2-B-a3-A3-C1-C2. The A1, A2 and A3 domains are interconnected by long linker...

    Authors: Divi Venkateswarlu
    Citation: BMC Structural Biology 2010 10:7
  25. Catalytic activity of influenza neuraminidase (NA) facilitates elution of progeny virions from infected cells and prevents their self-aggregation mediated by the catalytic site located in the body region. Rese...

    Authors: Ambarnil Ghosh, Ashesh Nandy and Papiya Nandy
    Citation: BMC Structural Biology 2010 10:6
  26. Template-target sequence alignment and loop modeling are key components of protein comparative modeling. Short loops can be predicted with high accuracy using structural fragments from other, not necessairly h...

    Authors: Michal Jamroz and Andrzej Kolinski
    Citation: BMC Structural Biology 2010 10:5
  27. The emergence of structural genomics presents significant challenges in the annotation of biologically uncharacterized proteins. Unfortunately, our ability to analyze these proteins is restricted by the limite...

    Authors: Shirley Wu, Tianyun Liu and Russ B Altman
    Citation: BMC Structural Biology 2010 10:4
  28. Sliding clamps, such as Proliferating Cell Nuclear Antigen (PCNA) in eukaryotes, are ring-shaped protein complexes that encircle DNA and enable highly processive DNA replication by serving as docking sites for...

    Authors: Randall McNally, Gregory D Bowman, Eric R Goedken, Mike O'Donnell and John Kuriyan
    Citation: BMC Structural Biology 2010 10:3
  29. The soluble guanylyl cyclase (sGC) is a heterodimeric enzyme that, upon activation by nitric oxide, stimulates the production of the second messenger cGMP. Each sGC subunit harbor four domains three of which a...

    Authors: Xiaolei Ma, Annie Beuve and Focco van den Akker
    Citation: BMC Structural Biology 2010 10:2
  30. Nonribosomal peptide synthetases (NRPSs) are multienzymatic, multidomain megasynthases involved in the biosynthesis of pharmaceutically important nonribosomal peptides. The peptaibol synthetase from Trichoderma v...

    Authors: Balachandran Manavalan, Senthil K Murugapiran, Gwang Lee and Sangdun Choi
    Citation: BMC Structural Biology 2010 10:1
  31. Setting the rules for the identification of a stable conformation of a protein is of utmost importance for the efficient generation of structures in computer simulation. For structure prediction, a considerabl...

    Authors: Ranjit Prasad Bahadur and Pinak Chakrabarti
    Citation: BMC Structural Biology 2009 9:76
  32. Many Gram-positive lactic acid bacteria (LAB) produce anti-bacterial peptides and small proteins called bacteriocins, which enable them to compete against other bacteria in the environment. These peptides fall...

    Authors: Changsoo Chang, Penny Coggill, Alex Bateman, Robert D Finn, Marcin Cymborowski, Zbyszek Otwinowski, Wladek Minor, Lour Volkart and Andrzej Joachimiak
    Citation: BMC Structural Biology 2009 9:75
  33. The equine infection anemia virus (EIAV) p9 Gag protein contains the late (L-) domain required for efficient virus release of nascent virions from the cell membrane of infected cell.

    Authors: Alok Sharma, Karsten Bruns, René Röder, Peter Henklein, Jörg Votteler, Victor Wray and Ulrich Schubert
    Citation: BMC Structural Biology 2009 9:74
  34. The triosephosphate isomerase (TIM)-barrel fold occurs frequently in the proteomes of different organisms, and the known TIM-barrel proteins have been found to play diverse functional roles. To accelerate the ...

    Authors: Jing-Na Si, Ren-Xiang Yan, Chuan Wang, Ziding Zhang and Xiao-Dong Su
    Citation: BMC Structural Biology 2009 9:73
  35. Recent advances on high-throughput technologies have produced a vast amount of protein sequences, while the number of high-resolution structures has seen a limited increase. This has impelled the production of...

    Authors: Patrick Aloy and Baldo Oliva
    Citation: BMC Structural Biology 2009 9:71
  36. The study of functional subfamilies of protein domain families and the identification of the residues which determine substrate specificity is an important question in the analysis of protein domains. One way ...

    Authors: Benjamin Georgi, Jörg Schultz and Alexander Schliep
    Citation: BMC Structural Biology 2009 9:68
  37. The carbonic anhydrases (CAs) are involved in inorganic carbon utilization. They have been classified into six evolutionary and structural families: α-, β-, γ-, δ-, ε-, ζ- CAs, with β-CAs present in higher pla...

    Authors: Yan-Bin Teng, Yong-Liang Jiang, Yong-Xing He, Wei-Wei He, Fu-Ming Lian, Yuxing Chen and Cong-Zhao Zhou
    Citation: BMC Structural Biology 2009 9:67
  38. Computational prediction of protein stability change due to single-site amino acid substitutions is of interest in protein design and analysis. We consider the following four ways to improve the performance of...

    Authors: Ayşegül Özen, Mehmet Gönen, Ethem Alpaydın and Türkan Haliloğlu
    Citation: BMC Structural Biology 2009 9:66
  39. Oligomeric enzymes can undergo a reversible loss of activity at low temperatures. One such enzyme is tryptophanase (Trpase) from Escherichia coli. Trpase is a pyridoxal phosphate (PLP)-dependent tetrameric enzyme...

    Authors: Anna Kogan, Garik Y Gdalevsky, Rivka Cohen-Luria, Yehuda Goldgur, Robert S Phillips, Abraham H Parola and Orna Almog
    Citation: BMC Structural Biology 2009 9:65
  40. Independent surveys of human gene promoter regions have demonstrated an overrepresentation of G3Xn 1G3Xn 2G3Xn 3G3 motifs which are known to be capable of forming intrastrand quadruple helix structures. In spite ...

    Authors: Federico Fogolari, Haritha Haridas, Alessandra Corazza, Paolo Viglino, Davide Corà, Michele Caselle, Gennaro Esposito and Luigi E Xodo
    Citation: BMC Structural Biology 2009 9:64
  41. Avidins are proteins with extraordinarily high ligand-binding affinity, a property which is used in a wide array of life science applications. Even though useful for biotechnology and nanotechnology, the biolo...

    Authors: Juha AE Määttä, Satu H Helppolainen, Vesa P Hytönen, Mark S Johnson, Markku S Kulomaa, Tomi T Airenne and Henri R Nordlund
    Citation: BMC Structural Biology 2009 9:63
  42. The novel A/H1N1 influenza virus, which recently emerged in North America is most closely related to North American H1N1/N2 swine viruses. Until the beginning of 2009, North American swine H1N1/N2 viruses have...

    Authors: Veljko Veljkovic, Henry L Niman, Sanja Glisic, Nevena Veljkovic, Vladimir Perovic and Claude P Muller
    Citation: BMC Structural Biology 2009 9:62