| | Other Issues: previous | next | latest | archiveSoftware GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures Thomas Laborde, Masaru Tomita, and Arun Krishnan PMCID: PMC2275735 PSAIA – Protein Structure and Interaction Analyzer Josip Mihel, Mile Šikić, Sanja Tomić, Branko Jeren, and Kristian Vlahoviček PMCID: PMC2364630 K2D2: Estimation of protein secondary structure from circular dichroism spectra Carolina Perez-Iratxeta and Miguel A Andrade-Navarro PMCID: PMC2397409 Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA Benjamin Bardiaux, Aymeric Bernard, Wolfgang Rieping, Michael Habeck, Thérèse E Malliavin, and Michael Nilges PMCID: PMC2432060 HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures Bosco K Ho and Franz Gruswitz PMCID: PMC2603037 PDBalert: automatic, recurrent remote homology tracking and protein structure prediction Vatsal Agarwal, Michael Remmert, Andreas Biegert, and Johannes Söding PMCID: PMC2605448 Research Articles 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, and Laurence Lins PMCID: PMC2254393 Preservation of protein clefts in comparative models David Piedra, Sergi Lois, and Xavier de la Cruz PMCID: PMC2249585 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, and Bingdong Sha PMCID: PMC2254625 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, and Anna V El'skaya PMCID: PMC2275276 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, Nataša Mitić, Lawrence R Gahan, and Luke W Guddat PMCID: PMC2267794 Comparative modelling by restraint-based conformational sampling Nicholas Furnham, Paul IW de Bakker, Swanand Gore, David F Burke, and Tom L Blundell PMCID: PMC2275734 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, and Igor Polikarpov PMCID: PMC2275733 Modeling structure and flexibility of Candida antarctica lipase B in organic solvents Peter Trodler and Jürgen Pleiss PMCID: PMC2262892 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, Päivi Pirilä, Dmitri I Svergun, and Petri Kursula PMCID: PMC2288786 Crystal structure of human IPS-1/MAVS/VISA/Cardif caspase activation recruitment domain Jane A Potter, Richard E Randall, and Garry L Taylor PMCID: PMC2291057 Structural deformation upon protein-protein interaction: A structural alphabet approach Juliette Martin, Leslie Regad, Hélène Lecornet, and Anne-Claude Camproux PMCID: PMC2315654 Crystal structures of PI3K-C2α PX domain indicate conformational change associated with ligand binding Gary N Parkinson, David Vines, Paul C Driscoll, and Snezana Djordjevic PMCID: PMC2292188 "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, and Stefano Pascarella PMCID: PMC2294123 Donor substrate recognition in the raffinose-bound E342A mutant of fructosyltransferase Bacillus subtilis levansucrase Guoyu Meng and Klaus Fütterer PMCID: PMC2277421 Solution structure of the Legionella pneumophila Mip-rapamycin complex Andreas Ceymann, Martin Horstmann, Philipp Ehses, Kristian Schweimer, Anne-Katrin Paschke, Michael Steinert, and Cornelius Faber PMCID: PMC2311308 Charge environments around phosphorylation sites in proteins James Kitchen, Rebecca E Saunders, and Jim Warwicker PMCID: PMC2291461 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, and Homme W Hellinga PMCID: PMC2315655 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, François Boudsocq, Virginie Gervais, Olivier Saurel, Marion Ciais, Christophe Cazaux, Jerzy Czaplicki, and Alain Milon PMCID: PMC2375893 Exploring allosteric coupling in the α-subunit of Heterotrimeric G proteins using evolutionary and ensemble-based approaches Kemal Sayar, Özlem Uğur, Tong Liu, Vincent J Hilser, and Ongun Onaran PMCID: PMC2422842 Improving the accuracy of template-based predictions by mixing and matching between initial models Tianyun Liu, Michal Guerquin, and Ram Samudrala PMCID: PMC2424052 Interactions between the quality control ubiquitin ligase CHIP and ubiquitin conjugating enzymes Zhen Xu, Ekta Kohli, Karl I Devlin, Michael Bold, Jay C Nix, and Saurav Misra PMCID: PMC2396629 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, and Ramanathan Sowdhamini PMCID: PMC2423364 Protecting role of cosolvents in protein denaturation by SDS: a structural study Catherine Michaux, Jenny Pouyez, Johan Wouters, and Gilbert G Privé PMCID: PMC2429906 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, and Roberto Sanchez PMCID: PMC2483983 Structural analysis of urate oxidase in complex with its natural substrate inhibited by cyanide: Mechanistic implications Laure Gabison, Thierry Prangé, Nathalie Colloc'h, Mohamed El Hajji, Bertrand Castro, and Mohamed Chiadmi PMCID: PMC2490695 Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase Sébastien Santini, Vincent Monchois, Nicolas Mouz, Cécile Sigoillot, Tristan Rousselle, Jean-Michel Claverie, and Chantal Abergel PMCID: PMC2515308 Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection Marc N Offman, Alexander L Tournier, and Paul A Bates PMCID: PMC2527322 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, René Ranzinger, William E Hull, Yuriy A Knirel, and Claus-Wilhelm von der Lieth PMCID: PMC2543016 Contact prediction in protein modeling: Scoring, folding and refinement of coarse-grained models Dorota Latek and Andrzej Kolinski PMCID: PMC2527566 Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces Kazuyoshi Ikeda, Takatsugu Hirokawa, Junichi Higo, and Kentaro Tomii PMCID: PMC2529298 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, and Roberto Gambari PMCID: PMC2543017 pi-Turns: types, systematics and the context of their occurrence in protein structures Bhaskar Dasgupta and Pinak Chakrabarti PMCID: PMC2559839 A method for probabilistic mapping between protein structure and function taxonomies through cross training Kshitiz Gupta, Vivek Sehgal, and Andre Levchenko PMCID: PMC2573881 Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms Bosco K Ho and David A Agard PMCID: PMC2569941 The crystal structure of the catalytic domain of a eukaryotic guanylate cyclase Jonathan A Winger, Emily R Derbyshire, Meindert H Lamers, Michael A Marletta, and John Kuriyan PMCID: PMC2576301 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, and Frederic Rousseau PMCID: PMC2585567 Flanking p10 contribution and sequence bias in matrix based epitope prediction: revisiting the assumption of independent binding pockets Christian S Parry PMCID: PMC2600787 A knowledge-based structure-discriminating function that requires only main-chain atom coordinates Yoshihide Makino and Nobuya Itoh PMCID: PMC2600639 Methodology Articles Fast dynamics perturbation analysis for prediction of protein functional sites Dengming Ming, Judith D Cohn, and Michael E Wall PMCID: PMC2276503 A multi-template combination algorithm for protein comparative modeling Jianlin Cheng PMCID: PMC2311309 Prediction of structural stability of short beta-hairpin peptides by molecular dynamics and knowledge-based potentials Karin Noy, Nir Kalisman, and Chen Keasar PMCID: PMC2427033 |
