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Editor-in-Chief
Melissa Norton, MD Biology Editor
Penelope Webb, PhD In-house Editor
Matthew Kaiser PhD
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| | BMC Structural Biology, Volume 9 |
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Methodology article
 
Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations
Patrick Aloy, Baldo Oliva
BMC Structural Biology 2009, 9:71 (16November2009)
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Research article
The structural and functional determinants of the Axin and Dishevelled DIX domains
Matthias T Ehebauer, Alfonso Martinez Arias
BMC Structural Biology 2009, 9:70 (12November2009)
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Software
Interacting with the biomolecular solvent accessible surface via a haptic feedback device
Matthew B Stocks, Steven Hayward, Stephen D Laycock
BMC Structural Biology 2009, 9:69 (27October2009)
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Research article
Partially-supervised protein subclass discovery with simultaneous annotation of functional residues
Benjamin Georgi, J rg Schultz, Alexander Schliep
BMC Structural Biology 2009, 9:68 (26October2009)
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Research article
Structural insights into the substrate tunnel of Saccharomyces cerevisiae carbonic anhydrase Nce103
Yan-Bin Teng, Yong-Liang Jiang, Yong-Xing He, Wei-Wei He, Fu-Ming Lian, Yuxing Chen, Cong-Zhao Zhou
BMC Structural Biology 2009, 9:67 (24October2009)
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Research article
Machine learning integration for predicting the effect of single amino acid substitutions on protein stability
Ay eg l  zen, Mehmet Gnen, Ethem Alpayd n, Trkan Halilo lu
BMC Structural Biology 2009, 9:66 (19October2009)
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Research article
Conformational changes and loose packing promote E. coli Tryptophanase cold lability
Anna Kogan, Garik Y Gdalevsky, Rivka Cohen-Luria, Yehuda Goldgur, Robert S Phillips, Abraham H Parola, Orna Almog
BMC Structural Biology 2009, 9:65 (8October2009)
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Research article
Molecular models for intrastrand DNA G-quadruplexes
Federico Fogolari, Haritha Haridas, Alessandra Corazza, Paolo Viglino, Davide Cor , Michele Caselle, Gennaro Esposito, Luigi E Xodo
BMC Structural Biology 2009, 9:64 (7October2009)
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Research article
Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis
Juha AE M tt, Satu H Helppolainen, Vesa P Hytnen, Mark S Johnson, Markku S Kulomaa, Tomi T Airenne, Henri R Nordlund
BMC Structural Biology 2009, 9:63 (29September2009)
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Research article
Identification of hemagglutinin structural domain and polymorphisms which may modulate swine H1N1 interactions with human receptor
Veljko Veljkovic, Henry L Niman, Sanja Glisic, Nevena Veljkovic, Vladimir Perovic, Claude P Muller
BMC Structural Biology 2009, 9:62 (28September2009)
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Research article
Mirrors in the PDB: left-handed  -turns guide design with D-amino acids
Srinivas Annavarapu, Vikas Nanda
BMC Structural Biology 2009, 9:61 (22September2009)
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Research article
Exploring protein structural dissimilarity to facilitate structure classification
Pooja Jain, Jonathan D Hirst
BMC Structural Biology 2009, 9:60 (19September2009)
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Research article
The Sam domain of the lipid phosphatase Ship2 adopts a common model to interact with Arap3-Sam and EphA2-Sam
Marilisa Leone, Jason Cellitti, Maurizio Pellecchia
BMC Structural Biology 2009, 9:59 (18September2009)
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Research article
Structural effects of clinically observed mutations in JAK2 exons 13-15: comparison with V617F and exon 12 mutations
Tai-Sung Lee, Wanlong Ma, Xi Zhang, Hagop Kantarjian, Maher Albitar
BMC Structural Biology 2009, 9:58 (10September2009)
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Research article
Low-resolution structural studies of human Stanniocalcin-1
Daniel M Trindade, J lio C Silva, Margareth S Navarro, Iris CL Torriani, Jrg Kobarg
BMC Structural Biology 2009, 9:57 (27August2009)
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Research article
Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallography
Kristina Lakomek, Achim Dickmanns, Matthias Kettwig, Henning Urlaub, Ralf Ficner, Torben Lbke
BMC Structural Biology 2009, 9:56 (25August2009)
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Research article
The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation
Jody A Winter, Panayiotis Christofi, Shaun Morroll, Karen A Bunting
BMC Structural Biology 2009, 9:55 (22August2009)
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Research article
The cyanobacterial cell division factor Ftn6 contains an N-terminal DnaD-like domain
Martial Marbouty, Cyril Saguez, Franck Chauvat
BMC Structural Biology 2009, 9:54 (21August2009)
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Research article
Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames)
Rafael M Cou ago, Milya Davlieva, Ulrich Strych, Ryan E Hill, Kurt L Krause
BMC Structural Biology 2009, 9:53 (20August2009)
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Software
A tool for calculating binding-site residues on proteins from PDB structures
Jing Hu, Changhui Yan
BMC Structural Biology 2009, 9:52 (3August2009)
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Methodology article
A generic method for assignment of reliability scores applied to solvent accessibility predictions
Bent Petersen, Thomas Nordahl Petersen, Pernille Andersen, Morten Nielsen, Claus Lundegaard
BMC Structural Biology 2009, 9:51 (31July2009)
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Methodology article
CRYSTALP2: sequence-based protein crystallization propensity prediction
Lukasz Kurgan, Ali A Razib, Sara Aghakhani, Scott Dick, Marcin Mizianty, Samad Jahandideh
BMC Structural Biology 2009, 9:50 (31July2009)
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Research article
Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome
Wayne Huggins, Sujit K Ghosh, Paul Wollenzien
BMC Structural Biology 2009, 9:49 (30July2009)
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Research article
A computational approach identifies two regions of Hepatitis C Virus E1 protein as interacting domains involved in viral fusion process
Roberto Bruni, Angela Costantino, Elena Tritarelli, Cinzia Marcantonio, Massimo Ciccozzi, Maria Rapicetta, Gamal El Sawaf, Alessandro Giuliani, Anna Rita Ciccaglione
BMC Structural Biology 2009, 9:48 (29July2009)
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Research article
An in silico study of the molecular basis of B-RAF activation and conformational stability
Filip F Fratev, Svava  sk J nsdttir
BMC Structural Biology 2009, 9:47 (22July2009)
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Research article
Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; a widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase families
Esben M Quistgaard, S ren S Thirup
BMC Structural Biology 2009, 9:46 (13July2009)
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Research article
Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model
Wenjun Zheng, Mustafa Tekpinar
BMC Structural Biology 2009, 9:45 (10July2009)
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Research article
Amyloidogenic determinants are usually not buried
Kimon K Frousios, Vassiliki A Iconomidou, Carolina-Maria Karletidi, Stavros J Hamodrakas
BMC Structural Biology 2009, 9:44 (9July2009)
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Research article
Exon 6 of human JAG1 encodes a conserved structural unit
Alessandro Pintar, Corrado Guarnaccia, Somdutta Dhir, S ndor Pongor
BMC Structural Biology 2009, 9:43 (8July2009)
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Research article
Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases
Apirat Chaikuad, R Leo Brady
BMC Structural Biology 2009, 9:42 (3July2009)
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Research article
Improved estimation of structure predictor quality
Kevin W DeRonne, George Karypis
BMC Structural Biology 2009, 9:41 (30June2009)
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Research article
Structural and phylogenetic analysis of a conserved actinobacteria-specific protein (ASP1; SCO1997) from Streptomyces coelicolor
Beile Gao, Seiji Sugiman-Marangos, Murray S Junop, Radhey S Gupta
BMC Structural Biology 2009, 9:40 (10June2009)
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Research article
Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking
P Benjamin Juhl, Peter Trodler, Sadhna Tyagi, Jrgen Pleiss
BMC Structural Biology 2009, 9:39 (3June2009)
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Research article
Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase
Peter Trodler, Rolf D Schmid, Jrgen Pleiss
BMC Structural Biology 2009, 9:38 (28May2009)
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Research article
Analysis of proteins with the 'hot dog' fold: Prediction of function and identification of catalytic residues of hypothetical proteins
Lakshmi S Pidugu, Koustav Maity, Karthikeyan Ramaswamy, Namita Surolia, Kaza Suguna
BMC Structural Biology 2009, 9:37 (28May2009)
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Research article
On the mechanism of autoinhibition of the RhoA-specific nucleotide exchange factor PDZRhoGEF
Meiying Zheng, Tomasz Cierpicki, Ko Momotani, Mykhaylo V Artamonov, Urszula Derewenda, John H Bushweller, Avril V Somlyo, Zygmunt S Derewenda
BMC Structural Biology 2009, 9:36 (21May2009)
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Research article
QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information
Pascal Benkert, Torsten Schwede, Silvio CE Tosatto
BMC Structural Biology 2009, 9:35 (20May2009)
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Research article
Universal partitioning of the hierarchical fold network of 50-residue segments in proteins
Jun-ichi Ito, Yuki Sonobe, Kazuyoshi Ikeda, Kentaro Tomii, Junichi Higo
BMC Structural Biology 2009, 9:34 (20May2009)
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Research article
Improving protein structure similarity searches using domain boundaries based on conserved sequence information
Kenneth Evan Thompson, Yanli Wang, Tom Madej, Stephen H Bryant
BMC Structural Biology 2009, 9:33 (19May2009)
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Research article
Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein
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-Lombard a, Alfred A Antson
BMC Structural Biology 2009, 9:32 (19May2009)
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Research article
Interaction of perfluorooctanoic acid with human serum albumin
Ling-Ling Wu, Hong-Wen Gao, Nai-Yun Gao, Fang-Fang Chen, Ling Chen
BMC Structural Biology 2009, 9:31 (14May2009)
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Research article
Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks
Munazah Andrabi, Kenji Mizuguchi, Akinori Sarai, Shandar Ahmad
BMC Structural Biology 2009, 9:30 (13May2009)
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Research article
Three dimensional shape comparison of flexible proteins using the local-diameter descriptor
Yi Fang, Yu-Shen Liu, Karthik Ramani
BMC Structural Biology 2009, 9:29 (12May2009)
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Research article
Improving consensus contact prediction via server correlation reduction
Xin Gao, Dongbo Bu, Jinbo Xu, Ming Li
BMC Structural Biology 2009, 9:28 (6May2009)
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Software
PTools: an opensource molecular docking library
Adrien Saladin, S bastien Fiorucci, Pierre Poulain, Chantal Prvost, Martin Zacharias
BMC Structural Biology 2009, 9:27 (1May2009)
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Research article
Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors
Satoshi Fukuchi, Keiichi Homma, Yoshiaki Minezaki, Takashi Gojobori, Ken Nishikawa
BMC Structural Biology 2009, 9:26 (30April2009)
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Research article
Context dependent reference states of solvent accessibility derived from native protein structures and assessed by predictability analysis
Hemajit Singh, Shandar Ahmad
BMC Structural Biology 2009, 9:25 (27April2009)
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Research article
Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs
Arvind Marathe, Deepti Karandur, Manju Bansal
BMC Structural Biology 2009, 9:24 (24April2009)
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Methodology article
Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis
Gergely Csaba, Fabian Birzele, Ralf Zimmer
BMC Structural Biology 2009, 9:23 (17April2009)
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Research article
Analysis of the impact of solvent on contacts prediction in proteins
Sergey A Samsonov, Joan Teyra, Gerd Anders, M Teresa Pisabarro
BMC Structural Biology 2009, 9:22 (15April2009)
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Research article
Characterization of conserved properties of hemagglutinin of H5N1 and human influenza viruses: possible consequences for therapy and infection control
Veljko Veljkovic, Nevena Veljkovic, Claude P Muller, Sybille Mller, Sanja Glisic, Vladimir Perovic, Heinz Khler
BMC Structural Biology 2009, 9:21 (7April2009)
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Research article
Relationship between chemical shift value and accessible surface area for all amino acid atoms
Wim F Vranken, Wolfgang Rieping
BMC Structural Biology 2009, 9:20 (2April2009)
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Software
ProteinShader: illustrative rendering of macromolecules
Joseph R Weber
BMC Structural Biology 2009, 9:19 (30March2009)
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Methodology article
Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra
Carlos Oscar S Sorzano, Abraham Otero, Estefana M Olmos, Jos Mara Carazo
BMC Structural Biology 2009, 9:18 (26March2009)
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Research article
Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA  Implications for the catalytic mechanism of parvulins
Outi Heikkinen, Raili Seppala, Helena Tossavainen, Sami Heikkinen, Harri Koskela, Perttu Permi, Ilkka Kilpelinen
BMC Structural Biology 2009, 9:17 (24March2009)
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Research article
Rational mutagenesis to support structure-based drug design: MAPKAP kinase 2 as a case study
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, Robert V Talanian, Ramkrishna Sadhukhan
BMC Structural Biology 2009, 9:16 (18March2009)
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Methodology article
Structural pattern matching of nonribosomal peptides
Sgol ne Caboche, Maude Pupin, Valrie Leclre, Phillipe Jacques, Gregory Kucherov
BMC Structural Biology 2009, 9:15 (18March2009)
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Research article
Implications of the structure of human uridine phosphorylase 1 on the development of novel inhibitors for improving the therapeutic window of fluoropyrimidine chemotherapy
Tarmo P Roosild, Samantha Castronovo, Michael Fabbiani, Giuseppe Pizzorno
BMC Structural Biology 2009, 9:14 (16March2009)
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Database
Database of ligand-induced domain movements in enzymes
Guoying Qi, Steven Hayward
BMC Structural Biology 2009, 9:13 (6March2009)
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Research article
Improving consensus structure by eliminating averaging artifacts
Dukka B KC
BMC Structural Biology 2009, 9:12 (6March2009)
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Research article
The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops
Andrew F Neuwald
BMC Structural Biology 2009, 9:11 (5March2009)
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Research article
An automatic method for assessing structural importance of amino acid positions
Michael I Sadowski, David T Jones
BMC Structural Biology 2009, 9:10 (4March2009)
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Research article
An unexpected phosphate binding site in Glyceraldehyde 3-Phosphate Dehydrogenase: Crystal structures of apo, holo and ternary complex of Cryptosporidium parvum enzyme
William J Cook, Olga Senkovich, Debasish Chattopadhyay
BMC Structural Biology 2009, 9:9 (25February2009)
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Research article
Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks
Moitrayee Bhattacharyya, Saraswathi Vishveshwara
BMC Structural Biology 2009, 9:8 (25February2009)
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Research article
The structure of the leukemia drug imatinib bound to human quinone reductase 2 (NQO2)
Jonathan A Winger, Oliver Hantschel, Giulio Superti-Furga, John Kuriyan
BMC Structural Biology 2009, 9:7 (24February2009)
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Research article
Comparison of molecular dynamics and superfamily spaces of protein domain deformation
Javier A Velzquez-Muriel, Manuel Rueda, Isabel Cuesta, Alberto Pascual-Montano, Modesto Orozco, Jos-Mara Carazo
BMC Structural Biology 2009, 9:6 (17February2009)
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Research article
Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks
Ian Walsh, Davide Ba , Alberto JM Martin, Catherine Mooney, Alessandro Vullo, Gianluca Pollastri
BMC Structural Biology 2009, 9:5 (30January2009)
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Research article
Analysing the origin of long-range interactions in proteins using lattice models
Orly Noivirt-Brik, Ron Unger, Amnon Horovitz
BMC Structural Biology 2009, 9:4 (29January2009)
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Research article
Molecular models of human P-glycoprotein in two different catalytic states
Jean-Paul Becker, Grgoire Depret, Fran oise Van Bambeke, Paul M Tulkens, Martine Prvost
BMC Structural Biology 2009, 9:3 (22January2009)
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Research article
Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm
Takuji Oyama, Hayato Oka, Kouta Mayanagi, Tsuyoshi Shirai, Kyoko Matoba, Ryosuke Fujikane, Yoshizumi Ishino, Kosuke Morikawa
BMC Structural Biology 2009, 9:2 (22January2009)
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Research article
Mesothelin, Stereocilin, and Otoancorin are predicted to have superhelical structures with ARM-type repeats
Bangalore K Sathyanarayana, Yoonsoo Hahn, Manish S Patankar, Ira Pastan, Byungkook Lee
BMC Structural Biology 2009, 9:1 (7January2009)
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