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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 8 |
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Research article
  
Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families
Ratna R Thangudu, Malini Manoharan, N Srinivasan, Fr dric Cadet, R Sowdhamini, Bernard Offmann
BMC Structural Biology 2008, 8:55 (26December2008)
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Research article
Knottin cyclization: impact on structure and dynamics
Annie Heitz, Olga Avrutina, Dung Le-Nguyen, Ulf Diederichsen, Jean-Fran ois Hernandez, Jr me Gracy, Harald Kolmar, Laurent Chiche
BMC Structural Biology 2008, 8:54 (12December2008)
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Research article
Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys
Dan M Bolser, Ioannis Filippis, Henning Stehr, Jose Duarte, Michael Lappe
BMC Structural Biology 2008, 8:53 (8December2008)
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Research article
SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs
Arlo Randall, Pierre Baldi
BMC Structural Biology 2008, 8:52 (3December2008)
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Software
PDBalert: automatic, recurrent remote homology tracking and protein structure prediction
Vatsal Agarwal, Michael Remmert, Andreas Biegert, Johannes S ding
BMC Structural Biology 2008, 8:51 (25November2008)
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Research article
Ligand-induced conformational changes in a thermophilic ribose-binding protein
Matthew J Cuneo, Lorena S Beese, Homme W Hellinga
BMC Structural Biology 2008, 8:50 (19November2008)
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Software
HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures
Bosco K Ho, Franz Gruswitz
BMC Structural Biology 2008, 8:49 (14November2008)
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Research article
Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site
Katarzyna H Kaminska, Mikihiko Kawai, Michal Boniecki, Ichizo Kobayashi, Janusz M Bujnicki
BMC Structural Biology 2008, 8:48 (14November2008)
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Database
LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs)
Tiandi Wei, Jing Gong, Ferdinand Jamitzky, Wolfgang M Heckl, Robert W Stark, Shaila C Rssle
BMC Structural Biology 2008, 8:47 (5November2008)
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Research article
A knowledge-based structure-discriminating function that requires only main-chain atom coordinates
Yoshihide Makino, Nobuya Itoh
BMC Structural Biology 2008, 8:46 (29October2008)
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Research article
Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites
T Andrew Binkowski, Andrzej Joachimiak
BMC Structural Biology 2008, 8:45 (27October2008)
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Research article
Flanking p10 contribution and sequence bias in matrix based epitope prediction: revisiting the assumption of independent binding pockets
Christian S Parry
BMC Structural Biology 2008, 8:44 (16October2008)
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Research article
Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure
Tom Lenaerts, Jesper Ferkinghoff-Borg, Francois Stricher, Luis Serrano, Joost WH Schymkowitz, Frederic Rousseau
BMC Structural Biology 2008, 8:43 (8October2008)
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Research article
Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms
Bosco K Ho, David A Agard
BMC Structural Biology 2008, 8:41 (7October2008)
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Research article
The crystal structure of the catalytic domain of a eukaryotic guanylate cyclase
Jonathan A Winger, Emily R Derbyshire, Meindert H Lamers, Michael A Marletta, John Kuriyan
BMC Structural Biology 2008, 8:42 (7October2008)
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Research article
A method for probabilistic mapping between protein structure and function taxonomies through cross training
Kshitiz Gupta, Vivek Sehgal, Andre Levchenko
BMC Structural Biology 2008, 8:40 (3October2008)
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Research article
pi-Turns: types, systematics and the context of their occurrence in protein structures
Bhaskar Dasgupta, Pinak Chakrabarti
BMC Structural Biology 2008, 8:39 (22September2008)
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Research article
Docking of molecules identified in bioactive medicinal plants extracts into the p50 NF-kappaB transcription factor: correlation with inhibition of NF-kappaB/DNA interactions and inhibitory effects on IL-8 gene expression
Laura Piccagli, Enrica Fabbri, Monica Borgatti, Valentino Bezzerri, Irene Mancini, Elena Nicolis, Maria C Dechecchi, Ilaria Lampronti, Giulio Cabrini, Roberto Gambari
BMC Structural Biology 2008, 8:38 (3September2008)
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Research article
Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces
Kazuyoshi Ikeda, Takatsugu Hirokawa, Junichi Higo, Kentaro Tomii
BMC Structural Biology 2008, 8:37 (13August2008)
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Research article
Contact prediction in protein modeling: Scoring, folding and refinement of coarse-grained models
Dorota Latek, Andrzej Kolinski
BMC Structural Biology 2008, 8:36 (11August2008)
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Research article
Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): Characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans
Stephan Herget, Philip V Toukach, Ren Ranzinger, William E Hull, Yuriy A Knirel, Claus-Wilhelm von der Lieth
BMC Structural Biology 2008, 8:35 (11August2008)
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Research article
Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection
Marc N Offman, Alexander L Tournier, Paul A Bates
BMC Structural Biology 2008, 8:34 (1August2008)
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Research article
Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase
Sbastien Santini, Vincent Monchois, Nicolas Mouz, Ccile Sigoillot, Tristan Rousselle, Jean-Michel Claverie, Chantal Abergel
BMC Structural Biology 2008, 8:33 (24July2008)
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Research article
Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: Mechanistic implications
Laure Gabison, Thierry Prang, Nathalie Colloc'h, Mohamed El Hajji, Bertrand Castro, Mohamed Chiadmi
BMC Structural Biology 2008, 8:32 (20July2008)
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Research article
Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure
Suvobrata Chakravarty, Sucheta Godbole, Bing Zhang, Seth Berger, Roberto Sanchez
BMC Structural Biology 2008, 8:31 (16July2008)
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Software
Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA
Benjamin Bardiaux, Aymeric Bernard, Wolfgang Rieping, Michael Habeck, Thr se E Malliavin, Michael Nilges
BMC Structural Biology 2008, 8:30 (5June2008)
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Research article
Protecting role of cosolvents in protein denaturation by SDS: a structural study
Catherine Michaux, Jenny Pouyez, Johan Wouters, Gilbert G Priv
BMC Structural Biology 2008, 8:29 (3June2008)
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Research article
CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations
Sankaran Sandhya, Barah Pankaj, Madabosse Kande Govind, Bernard Offmann, Narayanaswamy Srinivasan, Ramanathan Sowdhamini
BMC Structural Biology 2008, 8:28 (31May2008)
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Methodology article
Prediction of structural stability of short beta-hairpin peptides by molecular dynamics and knowledge-based potentials
Karin Noy, Nir Kalisman, Chen Keasar
BMC Structural Biology 2008, 8:27 (29May2008)
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Research article
Interactions between the quality control ubiquitin ligase CHIP and ubiquitin conjugating enzymes
Zhen Xu, Ekta Kohli, Karl I Devlin, Michael Bold, Jay C Nix, Saurav Misra
BMC Structural Biology 2008, 8:26 (16May2008)
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Software
K2D2: Estimation of protein secondary structure from circular dichroism spectra
Carolina Perez-Iratxeta, Miguel A Andrade-Navarro
BMC Structural Biology 2008, 8:25 (13May2008)
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Research article
Improving the accuracy of template-based predictions by mixing and matching between initial models
Tianyun Liu, Michal Guerquin, Ram Samudrala
BMC Structural Biology 2008, 8:24 (5May2008)
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Research article
Exploring allosteric coupling in the  -subunit of Heterotrimeric G proteins using evolutionary and ensemble-based approaches
Kemal Sayar,  zlem U ur, Tong Liu, Vincent J Hilser, Ongun Onaran
BMC Structural Biology 2008, 8:23 (2May2008)
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Research article
Structural insights on the pamoic acid and the 8 kDa domain of DNA polymerase beta complex: Towards the design of higher-affinity inhibitors
Corinne Hazan, Franois Boudsocq, Virginie Gervais, Olivier Saurel, Marion Ciais, Christophe Cazaux, Jerzy Czaplicki, Alain Milon
BMC Structural Biology 2008, 8:22 (16April2008)
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Software
PSAIA  Protein Structure and Interaction Analyzer
Josip Mihel, Mile  iki , Sanja Tomi, Branko Jeren, Kristian Vlahovi ek
BMC Structural Biology 2008, 8:21 (9April2008)
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Research article
The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog
Matthew J Cuneo, Yaji Tian, Malin Allert, Homme W Hellinga
BMC Structural Biology 2008, 8:20 (28March2008)
[Abstract] [Full text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Research article
Charge environments around phosphorylation sites in proteins
James Kitchen, Rebecca E Saunders, Jim Warwicker
BMC Structural Biology 2008, 8:19 (25March2008)
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Methodology article
A multi-template combination algorithm for protein comparative modeling
Jianlin Cheng
BMC Structural Biology 2008, 8:18 (17March2008)
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Research article
Solution structure of the Legionella pneumophila Mip-rapamycin complex
Andreas Ceymann, Martin Horstmann, Philipp Ehses, Kristian Schweimer, Anne-Katrin Paschke, Michael Steinert, Cornelius Faber
BMC Structural Biology 2008, 8:17 (17March2008)
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Research article
Donor substrate recognition in the raffinose-bound E342A mutant of fructosyltransferase Bacillus subtilis levansucrase
Guoyu Meng, Klaus F tterer
BMC Structural Biology 2008, 8:16 (17March2008)
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Software
GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures
Thomas Laborde, Masaru Tomita, Arun Krishnan
BMC Structural Biology 2008, 8:15 (7March2008)
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Research article
"Hot cores" in proteins: Comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms
Alessandro Paiardini, Riccardo Sali, Francesco Bossa, Stefano Pascarella
BMC Structural Biology 2008, 8:14 (29February2008)
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Research article
Crystal structures of PI3K-C2 PX domain indicate conformational change associated with ligand binding
Gary N Parkinson, David Vines, Paul C Driscoll, Snezana Djordjevic
BMC Structural Biology 2008, 8:13 (29February2008)
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Research article
Structural deformation upon protein-protein interaction: A structural alphabet approach
Juliette Martin, Leslie Regad, Hlne Lecornet, Anne-Claude Camproux
BMC Structural Biology 2008, 8:12 (28February2008)
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Research article
Crystal structure of human IPS-1/MAVS/VISA/Cardif caspase activation recruitment domain
Jane A Potter, Richard E Randall, Garry L Taylor
BMC Structural Biology 2008, 8:11 (28February2008)
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Research article
Interaction between the C-terminal region of human myelin basic protein and calmodulin: analysis of complex formation and solution structure
Viivi Majava, Maxim V Petoukhov, Nobuhiro Hayashi, P ivi Piril, Dmitri I Svergun, Petri Kursula
BMC Structural Biology 2008, 8:10 (19February2008)
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Research article
Modeling structure and flexibility of Candida antarctica lipase B in organic solvents
Peter Trodler, Jrgen Pleiss
BMC Structural Biology 2008, 8:9 (6February2008)
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Research article
Structural basis of GC-1 selectivity for thyroid hormone receptor isoforms
Lucas Bleicher, Ricardo Aparicio, Fabio M Nunes, Leandro Martinez, Sandra M Gomes Dias, Ana Carolina Migliorini Figueira, Maria Auxiliadora Morim Santos, Walter H Venturelli, Rosangela da Silva, Paulo Marcos Donate, Francisco AR Neves, Luiz A Simeoni, John D Baxter, Paul Webb, Munir S Skaf, Igor Polikarpov
BMC Structural Biology 2008, 8:8 (31January2008)
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Research article
Comparative modelling by restraint-based conformational sampling
Nicholas Furnham, Paul IW de Bakker, Swanand Gore, David F Burke, Tom L Blundell
BMC Structural Biology 2008, 8:7 (31January2008)
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Research article
Crystal structures of a purple acid phosphatase, representing different steps of this enzyme's catalytic cycle
Gerhard Schenk, Tristan W Elliott, Eleanor Leung, Lyle E Carrington, Nata a Miti, Lawrence R Gahan, Luke W Guddat
BMC Structural Biology 2008, 8:6 (31January2008)
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Methodology article
Fast dynamics perturbation analysis for prediction of protein functional sites
Dengming Ming, Judith D Cohn, Michael E Wall
BMC Structural Biology 2008, 8:5 (30January2008)
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Research article
Multiple molecular dynamics simulation of the isoforms of human translation elongation factor 1A reveals reversible fluctuations between "open" and "closed" conformations and suggests specific for eEF1A1 affinity for Ca2+-calmodulin
Dmitry S Kanibolotsky, Oleksandra V Novosyl'na, Catherine M Abbott, Boris S Negrutskii, Anna V El'skaya
BMC Structural Biology 2008, 8:4 (25January2008)
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Research article
The crystal structure of the putative peptide-binding fragment from the human Hsp40 protein Hdj1
Junbin Hu, Yunkun Wu, Jingzhi Li, Xinguo Qian, Zhengqing Fu, Bingdong Sha
BMC Structural Biology 2008, 8:3 (22January2008)
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Research article
Preservation of protein clefts in comparative models
David Piedra, Sergi Lois, Xavier de la Cruz
BMC Structural Biology 2008, 8:2 (16January2008)
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Research article
Distantly related lipocalins share two conserved clusters of hydrophobic residues: use in homology modeling
Benoit Adam, Benoit Charloteaux, Jerome Beaufays, Luc Vanhamme, Edmond Godfroid, Robert Brasseur, Laurence Lins
BMC Structural Biology 2008, 8:1 (11January2008)
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