Volume 9, issue 1, December 2009
76 articles in this issue
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The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes
Authors (first, second and last of 9)
- Changsoo Chang
- Penny Coggill
- Andrzej Joachimiak
- Content type: Research article
- Open Access
- Published: 17 December 2009
- Article: 75
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Solution structure of the Equine Infectious Anemia Virus p9 protein: a rationalization of its different ALIX binding requirements compared to the analogous HIV-p6 protein
Authors (first, second and last of 7)
- Alok Sharma
- Karsten Bruns
- Ulrich Schubert
- Content type: Research article
- Open Access
- Published: 17 December 2009
- Article: 74
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TIM-Finder: A new method for identifying TIM-barrel proteins
Authors (first, second and last of 5)
- Jing-Na Si
- Ren-Xiang Yan
- Xiao-Dong Su
- Content type: Methodology article
- Open Access
- Published: 14 December 2009
- Article: 73
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Prediction of calcium-binding sites by combining loop-modeling with machine learning
Authors
- Tianyun Liu
- Russ B Altman
- Content type: Research article
- Open Access
- Published: 11 December 2009
- Article: 72
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Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations
Authors
- Patrick Aloy
- Baldo Oliva
- Content type: Methodology article
- Open Access
- Published: 16 November 2009
- Article: 71
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The structural and functional determinants of the Axin and Dishevelled DIX domains
Authors
- Matthias T Ehebauer
- Alfonso Martinez Arias
- Content type: Research article
- Open Access
- Published: 12 November 2009
- Article: 70
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Interacting with the biomolecular solvent accessible surface via a haptic feedback device
Authors
- Matthew B Stocks
- Steven Hayward
- Stephen D Laycock
- Content type: Software
- Open Access
- Published: 27 October 2009
- Article: 69
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Partially-supervised protein subclass discovery with simultaneous annotation of functional residues
Authors
- Benjamin Georgi
- Jörg Schultz
- Alexander Schliep
- Content type: Research article
- Open Access
- Published: 26 October 2009
- Article: 68
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Structural insights into the substrate tunnel of Saccharomyces cerevisiae carbonic anhydrase Nce103
Authors (first, second and last of 7)
- Yan-Bin Teng
- Yong-Liang Jiang
- Cong-Zhao Zhou
- Content type: Research article
- Open Access
- Published: 24 October 2009
- Article: 67
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Machine learning integration for predicting the effect of single amino acid substitutions on protein stability
Authors (first, second and last of 4)
- Ayşegül Özen
- Mehmet Gönen
- Türkan Haliloğlu
- Content type: Research article
- Open Access
- Published: 19 October 2009
- Article: 66
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Conformational changes and loose packing promote E. coli Tryptophanase cold lability
Authors (first, second and last of 7)
- Anna Kogan
- Garik Y Gdalevsky
- Orna Almog
- Content type: Research article
- Open Access
- Published: 08 October 2009
- Article: 65
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Molecular models for intrastrand DNA G-quadruplexes
Authors (first, second and last of 8)
- Federico Fogolari
- Haritha Haridas
- Luigi E Xodo
- Content type: Research article
- Open Access
- Published: 07 October 2009
- Article: 64
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Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis
Authors (first, second and last of 7)
- Juha AE Määttä
- Satu H Helppolainen
- Henri R Nordlund
- Content type: Research article
- Open Access
- Published: 29 September 2009
- Article: 63
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Identification of hemagglutinin structural domain and polymorphisms which may modulate swine H1N1 interactions with human receptor
Authors (first, second and last of 6)
- Veljko Veljkovic
- Henry L Niman
- Claude P Muller
- Content type: Research article
- Open Access
- Published: 28 September 2009
- Article: 62
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Mirrors in the PDB: left-handed α-turns guide design with D-amino acids
Authors
- Srinivas Annavarapu
- Vikas Nanda
- Content type: Research article
- Open Access
- Published: 22 September 2009
- Article: 61
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Exploring protein structural dissimilarity to facilitate structure classification
Authors
- Pooja Jain
- Jonathan D Hirst
- Content type: Research article
- Open Access
- Published: 19 September 2009
- Article: 60
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The Sam domain of the lipid phosphatase Ship2 adopts a common model to interact with Arap3-Sam and EphA2-Sam
Authors
- Marilisa Leone
- Jason Cellitti
- Maurizio Pellecchia
- Content type: Research article
- Open Access
- Published: 18 September 2009
- Article: 59
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Structural effects of clinically observed mutations in JAK2 exons 13-15: comparison with V617F and exon 12 mutations
Authors (first, second and last of 5)
- Tai-Sung Lee
- Wanlong Ma
- Maher Albitar
- Content type: Research article
- Open Access
- Published: 10 September 2009
- Article: 58
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Low-resolution structural studies of human Stanniocalcin-1
Authors (first, second and last of 5)
- Daniel M Trindade
- Júlio C Silva
- Jörg Kobarg
- Content type: Research article
- Open Access
- Published: 27 August 2009
- Article: 57
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Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallography
Authors (first, second and last of 6)
- Kristina Lakomek
- Achim Dickmanns
- Torben Lübke
- Content type: Research article
- Open Access
- Published: 25 August 2009
- Article: 56
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The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation
Authors (first, second and last of 4)
- Jody A Winter
- Panayiotis Christofi
- Karen A Bunting
- Content type: Research article
- Open Access
- Published: 22 August 2009
- Article: 55
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The cyanobacterial cell division factor Ftn6 contains an N-terminal DnaD-like domain
Authors
- Martial Marbouty
- Cyril Saguez
- Franck Chauvat
- Content type: Research article
- Open Access
- Published: 21 August 2009
- Article: 54
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Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames)
Authors (first, second and last of 5)
- Rafael M Couñago
- Milya Davlieva
- Kurt L Krause
- Content type: Research article
- Open Access
- Published: 20 August 2009
- Article: 53
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A tool for calculating binding-site residues on proteins from PDB structures
Authors
- Jing Hu
- Changhui Yan
- Content type: Software
- Open Access
- Published: 03 August 2009
- Article: 52
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A generic method for assignment of reliability scores applied to solvent accessibility predictions
Authors (first, second and last of 5)
- Bent Petersen
- Thomas Nordahl Petersen
- Claus Lundegaard
- Content type: Methodology article
- Open Access
- Published: 31 July 2009
- Article: 51
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CRYSTALP2: sequence-based protein crystallization propensity prediction
Authors (first, second and last of 6)
- Lukasz Kurgan
- Ali A Razib
- Samad Jahandideh
- Content type: Methodology article
- Open Access
- Published: 31 July 2009
- Article: 50
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Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome
Authors
- Wayne Huggins
- Sujit K Ghosh
- Paul Wollenzien
- Content type: Research article
- Open Access
- Published: 30 July 2009
- Article: 49
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A computational approach identifies two regions of Hepatitis C Virus E1 protein as interacting domains involved in viral fusion process
Authors (first, second and last of 9)
- Roberto Bruni
- Angela Costantino
- Anna Rita Ciccaglione
- Content type: Research article
- Open Access
- Published: 29 July 2009
- Article: 48
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An in silico study of the molecular basis of B-RAF activation and conformational stability
Authors
- Filip F Fratev
- Svava Ósk Jónsdóttir
- Content type: Research article
- Open Access
- Published: 22 July 2009
- Article: 47
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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
Authors
- Esben M Quistgaard
- Søren S Thirup
- Content type: Research article
- Open Access
- Published: 13 July 2009
- Article: 46
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Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model
Authors
- Wenjun Zheng
- Mustafa Tekpinar
- Content type: Research article
- Open Access
- Published: 10 July 2009
- Article: 45
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Amyloidogenic determinants are usually not buried
Authors (first, second and last of 4)
- Kimon K Frousios
- Vassiliki A Iconomidou
- Stavros J Hamodrakas
- Content type: Research article
- Open Access
- Published: 09 July 2009
- Article: 44
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Exon 6 of human JAG1 encodes a conserved structural unit
Authors (first, second and last of 4)
- Alessandro Pintar
- Corrado Guarnaccia
- Sándor Pongor
- Content type: Research article
- Open Access
- Published: 08 July 2009
- Article: 43
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Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases
Authors
- Apirat Chaikuad
- R Leo Brady
- Content type: Research article
- Open Access
- Published: 03 July 2009
- Article: 42
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Improved estimation of structure predictor quality
Authors
- Kevin W DeRonne
- George Karypis
- Content type: Research article
- Open Access
- Published: 30 June 2009
- Article: 41
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Structural and phylogenetic analysis of a conserved actinobacteria-specific protein (ASP1; SCO1997) from Streptomyces coelicolor
Authors (first, second and last of 4)
- Beile Gao
- Seiji Sugiman-Marangos
- Radhey S Gupta
- Content type: Research article
- Open Access
- Published: 10 June 2009
- Article: 40
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Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking
Authors (first, second and last of 4)
- P Benjamin Juhl
- Peter Trodler
- Jürgen Pleiss
- Content type: Research article
- Open Access
- Published: 03 June 2009
- Article: 39
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Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase
Authors
- Peter Trodler
- Rolf D Schmid
- Jürgen Pleiss
- Content type: Research article
- Open Access
- Published: 28 May 2009
- Article: 38
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Analysis of proteins with the 'hot dog' fold: Prediction of function and identification of catalytic residues of hypothetical proteins
Authors (first, second and last of 5)
- Lakshmi S Pidugu
- Koustav Maity
- Kaza Suguna
- Content type: Research article
- Open Access
- Published: 28 May 2009
- Article: 37
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On the mechanism of autoinhibition of the RhoA-specific nucleotide exchange factor PDZRhoGEF
Authors (first, second and last of 8)
- Meiying Zheng
- Tomasz Cierpicki
- Zygmunt S Derewenda
- Content type: Research article
- Open Access
- Published: 21 May 2009
- Article: 36
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QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information
Authors
- Pascal Benkert
- Torsten Schwede
- Silvio CE Tosatto
- Content type: Research article
- Open Access
- Published: 20 May 2009
- Article: 35
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Universal partitioning of the hierarchical fold network of 50-residue segments in proteins
Authors (first, second and last of 5)
- Jun-ichi Ito
- Yuki Sonobe
- Junichi Higo
- Content type: Research article
- Open Access
- Published: 20 May 2009
- Article: 34
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Improving protein structure similarity searches using domain boundaries based on conserved sequence information
Authors (first, second and last of 4)
- Kenneth Evan Thompson
- Yanli Wang
- Stephen H Bryant
- Content type: Research article
- Open Access
- Published: 19 May 2009
- Article: 33
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Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein
Authors (first, second and last of 11)
- C Leong Ng
- David G Waterman
- Alfred A Antson
- Content type: Research article
- Open Access
- Published: 19 May 2009
- Article: 32
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Interaction of perfluorooctanoic acid with human serum albumin
Authors (first, second and last of 5)
- Ling-Ling Wu
- Hong-Wen Gao
- Ling Chen
- Content type: Research article
- Open Access
- Published: 14 May 2009
- Article: 31
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Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks
Authors (first, second and last of 4)
- Munazah Andrabi
- Kenji Mizuguchi
- Shandar Ahmad
- Content type: Research article
- Open Access
- Published: 13 May 2009
- Article: 30
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Three dimensional shape comparison of flexible proteins using the local-diameter descriptor
Authors
- Yi Fang
- Yu-Shen Liu
- Karthik Ramani
- Content type: Research article
- Open Access
- Published: 12 May 2009
- Article: 29
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Improving consensus contact prediction via server correlation reduction
Authors (first, second and last of 4)
- Xin Gao
- Dongbo Bu
- Ming Li
- Content type: Research article
- Open Access
- Published: 06 May 2009
- Article: 28
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PTools: an opensource molecular docking library
Authors (first, second and last of 5)
- Adrien Saladin
- Sébastien Fiorucci
- Martin Zacharias
- Content type: Software
- Open Access
- Published: 01 May 2009
- Article: 27