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Database Database of ligand-induced domain movements in enzymes Guoying Qi and Steven Hayward PMCID: PMC2672080 Research article The structural and functional determinants of the Axin and Dishevelled DIX domains Matthias T Ehebauer and Alfonso Martinez Arias PMCID: PMC2780430 Software ProteinShader: illustrative rendering of macromolecules Joseph R Weber PMCID: PMC2672931 PTools: an opensource molecular docking library Adrien Saladin, Sébastien Fiorucci, Pierre Poulain, Chantal Prévost, and Martin Zacharias PMCID: PMC2685806 A tool for calculating binding-site residues on proteins from PDB structures Jing Hu and Changhui Yan PMCID: PMC2728722 Interacting with the biomolecular solvent accessible surface via a haptic feedback device Matthew B Stocks, Steven Hayward, and Stephen D Laycock 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 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 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 PMCID: PMC2661087 Analysing the origin of long-range interactions in proteins using lattice models Orly Noivirt-Brik, Ron Unger, and Amnon Horovitz 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 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 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 PMCID: PMC2655291 Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks Moitrayee Bhattacharyya and Saraswathi Vishveshwara 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 PMCID: PMC2662861 An automatic method for assessing structural importance of amino acid positions Michael I Sadowski and David T Jones 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 PMCID: PMC2656535 Improving consensus structure by eliminating averaging artifacts Dukka B KC 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 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 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 PMCID: PMC2678132 Relationship between chemical shift value and accessible surface area for all amino acid atoms Wim F Vranken and Wolfgang Rieping 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 PMCID: PMC2679750 Analysis of the impact of solvent on contacts prediction in proteins Sergey A Samsonov, Joan Teyra, Gerd Anders, and M Teresa Pisabarro 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 PMCID: PMC2687451 Context dependent reference states of solvent accessibility derived from native protein structures and assessed by predictability analysis Hemajit Singh and Shandar Ahmad 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 PMCID: PMC2687452 Improving consensus contact prediction via server correlation reduction Xin Gao, Dongbo Bu, Jinbo Xu, and Ming Li PMCID: PMC2689239 Three dimensional shape comparison of flexible proteins using the local-diameter descriptor Yi Fang, Yu-Shen Liu, and Karthik Ramani 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 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 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 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 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 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 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 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 PMCID: PMC2698920 Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase Peter Trodler, Rolf D Schmid, and Jürgen Pleiss 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 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 PMCID: PMC2714318 Improved estimation of structure predictor quality Kevin W DeRonne and George Karypis PMCID: PMC2712475 Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases Apirat Chaikuad and R Leo Brady PMCID: PMC2721837 Exon 6 of human JAG1 encodes a conserved structural unit Alessandro Pintar, Corrado Guarnaccia, Somdutta Dhir, and Sándor Pongor PMCID: PMC2725086 Amyloidogenic determinants are usually not buried Kimon K Frousios, Vassiliki A Iconomidou, Carolina-Maria Karletidi, and Stavros J Hamodrakas 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 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 PMCID: PMC2716378 An in silico study of the molecular basis of B-RAF activation and conformational stability Filip F Fratev and Svava Ósk Jónsdóttir 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 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 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 PMCID: PMC2743695 The cyanobacterial cell division factor Ftn6 contains an N-terminal DnaD-like domain Martial Marbouty, Cyril Saguez, and Franck Chauvat 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 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 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 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 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 PMCID: PMC2755476 Exploring protein structural dissimilarity to facilitate structure classification Pooja Jain and Jonathan D Hirst PMCID: PMC2754988 Mirrors in the PDB: left-handed α-turns guide design with D-amino acids Srinivas Annavarapu and Vikas Nanda 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 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 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 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 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 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 PMCID: PMC2775743 Partially-supervised protein subclass discovery with simultaneous annotation of functional residues Benjamin Georgi, Jörg Schultz, and Alexander Schliep PMCID: PMC2777906 Methodology Articles Structural pattern matching of nonribosomal peptides Ségolène Caboche, Maude Pupin, Valérie Leclère, Phillipe Jacques, and Gregory Kucherov 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 PMCID: PMC2683171 Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis Gergely Csaba, Fabian Birzele, and Ralf Zimmer PMCID: PMC2678134 CRYSTALP2: sequence-based protein crystallization propensity prediction Lukasz Kurgan, Ali A Razib, Sara Aghakhani, Scott Dick, Marcin Mizianty, and Samad Jahandideh 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 PMCID: PMC2725087 Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations Patrick Aloy and Baldo Oliva PMCID: PMC2783033 Other Issues: Journal List
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