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Volume 9;  2009
Database
Database of ligand-induced domain movements in enzymes
Guoying Qi and Steven Hayward
BMC Struct Biol. 2009; 9: 13. Published online 2009 March 6. doi: 10.1186/1472-6807-9-13.
PMCID: PMC2672080
Research article
The structural and functional determinants of the Axin and Dishevelled DIX domains
Matthias T Ehebauer and Alfonso Martinez Arias
BMC Struct Biol. 2009; 9: 70. Published online 2009 November 12. doi: 10.1186/1472-6807-9-70.
PMCID: PMC2780430
Software
ProteinShader: illustrative rendering of macromolecules
Joseph R Weber
BMC Struct Biol. 2009; 9: 19. Published online 2009 March 30. doi: 10.1186/1472-6807-9-19.
PMCID: PMC2672931
PTools: an opensource molecular docking library
Adrien Saladin, Sébastien Fiorucci, Pierre Poulain, Chantal Prévost, and Martin Zacharias
BMC Struct Biol. 2009; 9: 27. Published online 2009 May 1. doi: 10.1186/1472-6807-9-27.
PMCID: PMC2685806
A tool for calculating binding-site residues on proteins from PDB structures
Jing Hu and Changhui Yan
BMC Struct Biol. 2009; 9: 52. Published online 2009 August 3. doi: 10.1186/1472-6807-9-52.
PMCID: PMC2728722
Interacting with the biomolecular solvent accessible surface via a haptic feedback device
Matthew B Stocks, Steven Hayward, and Stephen D Laycock
BMC Struct Biol. 2009; 9: 69. Published online 2009 October 27. doi: 10.1186/1472-6807-9-69.
PMCID: PMC2774689
Research Articles
Mesothelin, Stereocilin, and Otoancorin are predicted to have superhelical structures with ARM-type repeats
Bangalore K Sathyanarayana, Yoonsoo Hahn, Manish S Patankar, Ira Pastan, and Byungkook Lee
BMC Struct Biol. 2009; 9: 1. Published online 2009 January 7. doi: 10.1186/1472-6807-9-1.
PMCID: PMC2628672
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, and Kosuke Morikawa
BMC Struct Biol. 2009; 9: 2. Published online 2009 January 22. doi: 10.1186/1472-6807-9-2.
PMCID: PMC2636818
Molecular models of human P-glycoprotein in two different catalytic states
Jean-Paul Becker, Grégoire Depret, Françoise Van Bambeke, Paul M Tulkens, and Martine Prévost
BMC Struct Biol. 2009; 9: 3. Published online 2009 January 22. doi: 10.1186/1472-6807-9-3.
PMCID: PMC2661087
Analysing the origin of long-range interactions in proteins using lattice models
Orly Noivirt-Brik, Ron Unger, and Amnon Horovitz
BMC Struct Biol. 2009; 9: 4. Published online 2009 January 29. doi: 10.1186/1472-6807-9-4.
PMCID: PMC2670300
Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks
Ian Walsh, Davide Baù, Alberto JM Martin, Catherine Mooney, Alessandro Vullo, and Gianluca Pollastri
BMC Struct Biol. 2009; 9: 5. Published online 2009 January 30. doi: 10.1186/1472-6807-9-5.
PMCID: PMC2654788
Comparison of molecular dynamics and superfamily spaces of protein domain deformation
Javier A Velázquez-Muriel, Manuel Rueda, Isabel Cuesta, Alberto Pascual-Montano, Modesto Orozco, and José-María Carazo
BMC Struct Biol. 2009; 9: 6. Published online 2009 February 17. doi: 10.1186/1472-6807-9-6.
PMCID: PMC2666742
The structure of the leukemia drug imatinib bound to human quinone reductase 2 (NQO2)
Jonathan A Winger, Oliver Hantschel, Giulio Superti-Furga, and John Kuriyan
BMC Struct Biol. 2009; 9: 7. Published online 2009 February 24. doi: 10.1186/1472-6807-9-7.
PMCID: PMC2655291
Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks
Moitrayee Bhattacharyya and Saraswathi Vishveshwara
BMC Struct Biol. 2009; 9: 8. Published online 2009 February 25. doi: 10.1186/1472-6807-9-8.
PMCID: PMC2656534
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, and Debasish Chattopadhyay
BMC Struct Biol. 2009; 9: 9. Published online 2009 February 25. doi: 10.1186/1472-6807-9-9.
PMCID: PMC2662861
An automatic method for assessing structural importance of amino acid positions
Michael I Sadowski and David T Jones
BMC Struct Biol. 2009; 9: 10. Published online 2009 March 4. doi: 10.1186/1472-6807-9-10.
PMCID: PMC2667441
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 Struct Biol. 2009; 9: 11. Published online 2009 March 5. doi: 10.1186/1472-6807-9-11.
PMCID: PMC2656535
Improving consensus structure by eliminating averaging artifacts
Dukka B KC
BMC Struct Biol. 2009; 9: 12. Published online 2009 March 6. doi: 10.1186/1472-6807-9-12.
PMCID: PMC2662860
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, and Giuseppe Pizzorno
BMC Struct Biol. 2009; 9: 14. Published online 2009 March 16. doi: 10.1186/1472-6807-9-14.
PMCID: PMC2664818
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, and Ramkrishna Sadhukhan
BMC Struct Biol. 2009; 9: 16. Published online 2009 March 18. doi: 10.1186/1472-6807-9-16.
PMCID: PMC2678131
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, and Ilkka Kilpeläinen
BMC Struct Biol. 2009; 9: 17. Published online 2009 March 24. doi: 10.1186/1472-6807-9-17.
PMCID: PMC2678132
Relationship between chemical shift value and accessible surface area for all amino acid atoms
Wim F Vranken and Wolfgang Rieping
BMC Struct Biol. 2009; 9: 20. Published online 2009 April 2. doi: 10.1186/1472-6807-9-20.
PMCID: PMC2678133
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 Müller, Sanja Glisic, Vladimir Perovic, and Heinz Köhler
BMC Struct Biol. 2009; 9: 21. Published online 2009 April 7. doi: 10.1186/1472-6807-9-21.
PMCID: PMC2679750
Analysis of the impact of solvent on contacts prediction in proteins
Sergey A Samsonov, Joan Teyra, Gerd Anders, and M Teresa Pisabarro
BMC Struct Biol. 2009; 9: 22. Published online 2009 April 15. doi: 10.1186/1472-6807-9-22.
PMCID: PMC2676287
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, and Manju Bansal
BMC Struct Biol. 2009; 9: 24. Published online 2009 April 24. doi: 10.1186/1472-6807-9-24.
PMCID: PMC2687451
Context dependent reference states of solvent accessibility derived from native protein structures and assessed by predictability analysis
Hemajit Singh and Shandar Ahmad
BMC Struct Biol. 2009; 9: 25. Published online 2009 April 27. doi: 10.1186/1472-6807-9-25.
PMCID: PMC2685369
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, and Ken Nishikawa
BMC Struct Biol. 2009; 9: 26. Published online 2009 April 30. doi: 10.1186/1472-6807-9-26.
PMCID: PMC2687452
Improving consensus contact prediction via server correlation reduction
Xin Gao, Dongbo Bu, Jinbo Xu, and Ming Li
BMC Struct Biol. 2009; 9: 28. Published online 2009 May 6. doi: 10.1186/1472-6807-9-28.
PMCID: PMC2689239
Three dimensional shape comparison of flexible proteins using the local-diameter descriptor
Yi Fang, Yu-Shen Liu, and Karthik Ramani
BMC Struct Biol. 2009; 9: 29. Published online 2009 May 12. doi: 10.1186/1472-6807-9-29.
PMCID: PMC2685140
Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks
Munazah Andrabi, Kenji Mizuguchi, Akinori Sarai, and Shandar Ahmad
BMC Struct Biol. 2009; 9: 30. Published online 2009 May 13. doi: 10.1186/1472-6807-9-30.
PMCID: PMC2693520
Interaction of perfluorooctanoic acid with human serum albumin
Ling-Ling Wu, Hong-Wen Gao, Nai-Yun Gao, Fang-Fang Chen, and Ling Chen
BMC Struct Biol. 2009; 9: 31. Published online 2009 May 14. doi: 10.1186/1472-6807-9-31.
PMCID: PMC2688008
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-Lombardía, and Alfred A Antson
BMC Struct Biol. 2009; 9: 32. Published online 2009 May 19. doi: 10.1186/1472-6807-9-32.
PMCID: PMC2695463
Improving protein structure similarity searches using domain boundaries based on conserved sequence information
Kenneth Evan Thompson, Yanli Wang, Tom Madej, and Stephen H Bryant
BMC Struct Biol. 2009; 9: 33. Published online 2009 May 19. doi: 10.1186/1472-6807-9-33.
PMCID: PMC2694201
Universal partitioning of the hierarchical fold network of 50-residue segments in proteins
Jun-ichi Ito, Yuki Sonobe, Kazuyoshi Ikeda, Kentaro Tomii, and Junichi Higo
BMC Struct Biol. 2009; 9: 34. Published online 2009 May 20. doi: 10.1186/1472-6807-9-34.
PMCID: PMC2693521
QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information
Pascal Benkert, Torsten Schwede, and Silvio CE Tosatto
BMC Struct Biol. 2009; 9: 35. Published online 2009 May 20. doi: 10.1186/1472-6807-9-35.
PMCID: PMC2709111
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, and Zygmunt S Derewenda
BMC Struct Biol. 2009; 9: 36. Published online 2009 May 21. doi: 10.1186/1472-6807-9-36.
PMCID: PMC2695464
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, and Kaza Suguna
BMC Struct Biol. 2009; 9: 37. Published online 2009 May 28. doi: 10.1186/1472-6807-9-37.
PMCID: PMC2698920
Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase
Peter Trodler, Rolf D Schmid, and Jürgen Pleiss
BMC Struct Biol. 2009; 9: 38. Published online 2009 May 28. doi: 10.1186/1472-6807-9-38.
PMCID: PMC2695465
Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking
P Benjamin Juhl, Peter Trodler, Sadhna Tyagi, and Jürgen Pleiss
BMC Struct Biol. 2009; 9: 39. Published online 2009 June 3. doi: 10.1186/1472-6807-9-39.
PMCID: PMC2699341
Structural and phylogenetic analysis of a conserved actinobacteria-specific protein (ASP1; SCO1997) from Streptomyces coelicolor
Beile Gao, Seiji Sugiman-Marangos, Murray S Junop, and Radhey S Gupta
BMC Struct Biol. 2009; 9: 40. Published online 2009 June 10. doi: 10.1186/1472-6807-9-40.
PMCID: PMC2714318
Improved estimation of structure predictor quality
Kevin W DeRonne and George Karypis
BMC Struct Biol. 2009; 9: 41. Published online 2009 June 30. doi: 10.1186/1472-6807-9-41.
PMCID: PMC2712475
Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases
Apirat Chaikuad and R Leo Brady
BMC Struct Biol. 2009; 9: 42. Published online 2009 July 3. doi: 10.1186/1472-6807-9-42.
PMCID: PMC2721837
Exon 6 of human JAG1 encodes a conserved structural unit
Alessandro Pintar, Corrado Guarnaccia, Somdutta Dhir, and Sándor Pongor
BMC Struct Biol. 2009; 9: 43. Published online 2009 July 8. doi: 10.1186/1472-6807-9-43.
PMCID: PMC2725086
Amyloidogenic determinants are usually not buried
Kimon K Frousios, Vassiliki A Iconomidou, Carolina-Maria Karletidi, and Stavros J Hamodrakas
BMC Struct Biol. 2009; 9: 44. Published online 2009 July 9. doi: 10.1186/1472-6807-9-44.
PMCID: PMC2714319
Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model
Wenjun Zheng and Mustafa Tekpinar
BMC Struct Biol. 2009; 9: 45. Published online 2009 July 10. doi: 10.1186/1472-6807-9-45.
PMCID: PMC2719638
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 and Søren S Thirup
BMC Struct Biol. 2009; 9: 46. Published online 2009 July 13. doi: 10.1186/1472-6807-9-46.
PMCID: PMC2716378
An in silico study of the molecular basis of B-RAF activation and conformational stability
Filip F Fratev and Svava Ósk Jónsdóttir
BMC Struct Biol. 2009; 9: 47. Published online 2009 July 22. doi: 10.1186/1472-6807-9-47.
PMCID: PMC2731097
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, and Anna Rita Ciccaglione
BMC Struct Biol. 2009; 9: 48. Published online 2009 July 29. doi: 10.1186/1472-6807-9-48.
PMCID: PMC2732612
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, and Paul Wollenzien
BMC Struct Biol. 2009; 9: 49. Published online 2009 July 30. doi: 10.1186/1472-6807-9-49.
PMCID: PMC2731775
Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames)
Rafael M Couñago, Milya Davlieva, Ulrich Strych, Ryan E Hill, and Kurt L Krause
BMC Struct Biol. 2009; 9: 53. Published online 2009 August 20. doi: 10.1186/1472-6807-9-53.
PMCID: PMC2743695
The cyanobacterial cell division factor Ftn6 contains an N-terminal DnaD-like domain
Martial Marbouty, Cyril Saguez, and Franck Chauvat
BMC Struct Biol. 2009; 9: 54. Published online 2009 August 21. doi: 10.1186/1472-6807-9-54.
PMCID: PMC2736966
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, and Karen A Bunting
BMC Struct Biol. 2009; 9: 55. Published online 2009 August 22. doi: 10.1186/1472-6807-9-55.
PMCID: PMC2737543
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, and Torben Lübke
BMC Struct Biol. 2009; 9: 56. Published online 2009 August 25. doi: 10.1186/1472-6807-9-56.
PMCID: PMC2739207
Low-resolution structural studies of human Stanniocalcin-1
Daniel M Trindade, Júlio C Silva, Margareth S Navarro, Iris CL Torriani, and Jörg Kobarg
BMC Struct Biol. 2009; 9: 57. Published online 2009 August 27. doi: 10.1186/1472-6807-9-57.
PMCID: PMC2744999
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, and Maher Albitar
BMC Struct Biol. 2009; 9: 58. Published online 2009 September 10. doi: 10.1186/1472-6807-9-58.
PMCID: PMC2749040
The Sam domain of the lipid phosphatase Ship2 adopts a common model to interact with Arap3-Sam and EphA2-Sam
Marilisa Leone, Jason Cellitti, and Maurizio Pellecchia
BMC Struct Biol. 2009; 9: 59. Published online 2009 September 18. doi: 10.1186/1472-6807-9-59.
PMCID: PMC2755476
Exploring protein structural dissimilarity to facilitate structure classification
Pooja Jain and Jonathan D Hirst
BMC Struct Biol. 2009; 9: 60. Published online 2009 September 19. doi: 10.1186/1472-6807-9-60.
PMCID: PMC2754988
Mirrors in the PDB: left-handed α-turns guide design with D-amino acids
Srinivas Annavarapu and Vikas Nanda
BMC Struct Biol. 2009; 9: 61. Published online 2009 September 22. doi: 10.1186/1472-6807-9-61.
PMCID: PMC2759939
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, and Claude P Muller
BMC Struct Biol. 2009; 9: 62. Published online 2009 September 28. doi: 10.1186/1472-6807-9-62.
PMCID: PMC2760557
Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis
Juha AE Määttä, Satu H Helppolainen, Vesa P Hytönen, Mark S Johnson, Markku S Kulomaa, Tomi T Airenne, and Henri R Nordlund
BMC Struct Biol. 2009; 9: 63. Published online 2009 September 29. doi: 10.1186/1472-6807-9-63.
PMCID: PMC2761383
Molecular models for intrastrand DNA G-quadruplexes
Federico Fogolari, Haritha Haridas, Alessandra Corazza, Paolo Viglino, Davide Corà, Michele Caselle, Gennaro Esposito, and Luigi E Xodo
BMC Struct Biol. 2009; 9: 64. Published online 2009 October 7. doi: 10.1186/1472-6807-9-64.
PMCID: PMC2768733
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, and Orna Almog
BMC Struct Biol. 2009; 9: 65. Published online 2009 October 8. doi: 10.1186/1472-6807-9-65.
PMCID: PMC2770544
Machine learning integration for predicting the effect of single amino acid substitutions on protein stability
Ayşegül Özen, Mehmet Gönen, Ethem Alpaydın, and Türkan Haliloğlu
BMC Struct Biol. 2009; 9: 66. Published online 2009 October 19. doi: 10.1186/1472-6807-9-66.
PMCID: PMC2777163
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, and Cong-Zhao Zhou
BMC Struct Biol. 2009; 9: 67. Published online 2009 October 24. doi: 10.1186/1472-6807-9-67.
PMCID: PMC2775743
Partially-supervised protein subclass discovery with simultaneous annotation of functional residues
Benjamin Georgi, Jörg Schultz, and Alexander Schliep
BMC Struct Biol. 2009; 9: 68. Published online 2009 October 26. doi: 10.1186/1472-6807-9-68.
PMCID: PMC2777906
Methodology Articles
Structural pattern matching of nonribosomal peptides
Ségolène Caboche, Maude Pupin, Valérie Leclère, Phillipe Jacques, and Gregory Kucherov
BMC Struct Biol. 2009; 9: 15. Published online 2009 March 18. doi: 10.1186/1472-6807-9-15.
PMCID: PMC2674430
Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra
Carlos Oscar S Sorzano, Abraham Otero, Estefanía M Olmos, and José María Carazo
BMC Struct Biol. 2009; 9: 18. Published online 2009 March 26. doi: 10.1186/1472-6807-9-18.
PMCID: PMC2683171
Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis
Gergely Csaba, Fabian Birzele, and Ralf Zimmer
BMC Struct Biol. 2009; 9: 23. Published online 2009 April 17. doi: 10.1186/1472-6807-9-23.
PMCID: PMC2678134
CRYSTALP2: sequence-based protein crystallization propensity prediction
Lukasz Kurgan, Ali A Razib, Sara Aghakhani, Scott Dick, Marcin Mizianty, and Samad Jahandideh
BMC Struct Biol. 2009; 9: 50. Published online 2009 July 31. doi: 10.1186/1472-6807-9-50.
PMCID: PMC2731098
A generic method for assignment of reliability scores applied to solvent accessibility predictions
Bent Petersen, Thomas Nordahl Petersen, Pernille Andersen, Morten Nielsen, and Claus Lundegaard
BMC Struct Biol. 2009; 9: 51. Published online 2009 July 31. doi: 10.1186/1472-6807-9-51.
PMCID: PMC2725087
Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations
Patrick Aloy and Baldo Oliva
BMC Struct Biol. 2009; 9: 71. Published online 2009 November 16. doi: 10.1186/1472-6807-9-71.
PMCID: PMC2783033
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