Bioinformatics, Vol 15, 305-308, Copyright © 1999 by Oxford University Press
P Gouet, E Courcelle, DI Stuart and F Metoz
MOTIVATION: The program ESPript (Easy Sequencing in PostScript) allows the
rapid visualization, via PostScript output, of sequences aligned with
popular programs such as CLUSTAL-W or GCG PILEUP. It can read secondary
structure files (such as that created by the program DSSP) to produce a
synthesis of both sequence and structural information. RESULTS: ESPript can
be run via a command file or a friendly html-based user interface. The
program calculates an homology score by columns of residues and can sort
this calculation by groups of sequences. It offers a palette of markers to
highlight important regions in the alignment. ESPript can also paste
information on residue conservation into coordinate files, for subsequent
visualization with a graphics program. AVAILABILITY: ESPript can be
accessed on its Web site at http://www.ipbs.fr/ESPript. Sources and
helpfiles can be downloaded via anonymous ftp from ftp.ipbs.fr. A tar file
is held in the directory pub/ESPript.
ARTICLES
ESPript: analysis of multiple sequence alignments in PostScript
Laboratory of Molecular Biophysics, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK. gouet@ipbs.fr
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C. Abergel, J. Rudinger-Thirion, R. Giege, and J.-M. Claverie Virus-Encoded Aminoacyl-tRNA Synthetases: Structural and Functional Characterization of Mimivirus TyrRS and MetRS J. Virol., November 15, 2007; 81(22): 12406 - 12417. [Abstract] [Full Text] [PDF]
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 L. M. Podust, J. P. von Kries, A. N. Eddine, Y. Kim, L. V. Yermalitskaya, R. Kuehne, H. Ouellet, T. Warrier, M. Altekoster, J.-S. Lee, et al. Small-Molecule Scaffolds for CYP51 Inhibitors Identified by High-Throughput Screening and Defined by X-Ray Crystallography Antimicrob. Agents Chemother., November 1, 2007; 51(11): 3915 - 3923. [Abstract] [Full Text] [PDF]
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Y. Shimomura, H. Kamikubo, Y. Nishi, T. Masako, M. Kataoka, Y. Kobayashi, K. Fukuyama, and Y. Takahashi Characterization and Crystallization of an IscU-type Scaffold Protein with Bound [2Fe 2S] Cluster from the Hyperthermophile, Aquifex aeolicus J. Biochem., November 1, 2007; 142(5): 577 - 586. [Abstract] [Full Text] [PDF]
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J. Benach, L. Wang, Y. Chen, C. K. Ho, S. Lee, J. Seetharaman, R. Xiao, T. B. Acton, G. T. Montelione, H. Deng, et al. Structural and Functional Studies of the Abundant Tegument Protein ORF52 from Murine Gammaherpesvirus 68 J. Biol. Chem., October 26, 2007; 282(43): 31534 - 31541. [Abstract] [Full Text] [PDF]
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K. A. Gangwer, D. J. Mushrush, D. L. Stauff, B. Spiller, M. S. McClain, T. L. Cover, and D. B. Lacy Crystal structure of the Helicobacter pylori vacuolating toxin p55 domain PNAS, October 9, 2007; 104(41): 16293 - 16298. [Abstract] [Full Text] [PDF]
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A. P. Bussink, D. Speijer, J. M. F. G. Aerts, and R. G. Boot Evolution of Mammalian Chitinase(-Like) Members of Family 18 Glycosyl Hydrolases Genetics, October 1, 2007; 177(2): 959 - 970. [Abstract] [Full Text] [PDF]
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M. Backovic, T. S. Jardetzky, and R. Longnecker Hydrophobic Residues That Form Putative Fusion Loops of Epstein-Barr Virus Glycoprotein B Are Critical for Fusion Activity J. Virol., September 1, 2007; 81(17): 9596 - 9600. [Abstract] [Full Text] [PDF]
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L. Barleben, S. Panjikar, M. Ruppert, J. Koepke, and J. Stockigt Molecular Architecture of Strictosidine Glucosidase: The Gateway to the Biosynthesis of the Monoterpenoid Indole Alkaloid Family PLANT CELL, September 1, 2007; 19(9): 2886 - 2897. [Abstract] [Full Text] [PDF]
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J. Lee, A. R. Feldman, B. Delmas, and M. Paetzel Crystal Structure of the VP4 Protease from Infectious Pancreatic Necrosis Virus Reveals the Acyl-Enzyme Complex for an Intermolecular Self-cleavage Reaction J. Biol. Chem., August 24, 2007; 282(34): 24928 - 24937. [Abstract] [Full Text] [PDF]
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 C. F. Sautel, D. Cannella, O. Bastien, S. Kieffer, D. Aldebert, J. Garin, I. Tardieux, H. Belrhali, and M.-A. Hakimi SET8-Mediated Methylations of Histone H4 Lysine 20 Mark Silent Heterochromatic Domains in Apicomplexan Genomes Mol. Cell. Biol., August 15, 2007; 27(16): 5711 - 5724. [Abstract] [Full Text] [PDF]
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K. Kim, J. Park, and S. Rhee Structural and Functional Basis for (S)-Allantoin Formation in the Ureide Pathway J. Biol. Chem., August 10, 2007; 282(32): 23457 - 23464. [Abstract] [Full Text] [PDF]
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R. S. De Silva, G. Kovacikova, W. Lin, R. K. Taylor, K. Skorupski, and F. J. Kull Crystal Structure of the Vibrio cholerae Quorum-Sensing Regulatory Protein HapR J. Bacteriol., August 1, 2007; 189(15): 5683 - 5691. [Abstract] [Full Text] [PDF]
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J. Wu, Y. Tao, M. Zhang, M. H. Howard, S. Gutteridge, and J. Ding Crystal Structures of Saccharomyces cerevisiae N-Myristoyltransferase with Bound Myristoyl-CoA and Inhibitors Reveal the Functional Roles of the N-terminal Region J. Biol. Chem., July 27, 2007; 282(30): 22185 - 22194. [Abstract] [Full Text] [PDF]
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 I. B. Quintero, C. L. Araujo, A. E. Pulkka, R. S. Wirkkala, A. M. Herrala, E.-L. Eskelinen, E. Jokitalo, P. A. Hellstrom, H. J. Tuominen, P. P. Hirvikoski, et al. Prostatic Acid Phosphatase Is Not a Prostate Specific Target Cancer Res., July 15, 2007; 67(14): 6549 - 6554. [Abstract] [Full Text] [PDF]
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Q. Yan, V. N. Malashkevich, A. Fedorov, E. Fedorov, E. Cao, J. W. Lary, J. L. Cole, S. G. Nathenson, and S. C. Almo Structure of CD84 provides insight into SLAM family function PNAS, June 19, 2007; 104(25): 10583 - 10588. [Abstract] [Full Text] [PDF]
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X. Tang, J. Wu, J. Sivaraman, and C. L. Hew Crystal Structures of Major Envelope Proteins VP26 and VP28 from White Spot Syndrome Virus Shed Light on Their Evolutionary Relationship J. Virol., June 15, 2007; 81(12): 6709 - 6717. [Abstract] [Full Text] [PDF]
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D. Maruyama, Y. Nishitani, T. Nonaka, A. Kita, T. A. Fukami, T. Mio, H. Yamada-Okabe, T. Yamada-Okabe, and K. Miki Crystal Structure of Uridine-diphospho-N-acetylglucosamine Pyrophosphorylase from Candida albicans and Catalytic Reaction Mechanism J. Biol. Chem., June 8, 2007; 282(23): 17221 - 17230. [Abstract] [Full Text] [PDF]
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G. Blanc, B. Font, D. Eichenberger, C. Moreau, S. Ricard-Blum, D. J. S. Hulmes, and C. Moali Insights into How CUB Domains Can Exert Specific Functions while Sharing a Common Fold: CONSERVED AND SPECIFIC FEATURES OF THE CUB1 DOMAIN CONTRIBUTE TO THE MOLECULAR BASIS OF PROCOLLAGEN C-PROTEINASE ENHANCER-1 ACTIVITY J. Biol. Chem., June 8, 2007; 282(23): 16924 - 16933. [Abstract] [Full Text] [PDF]
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R. Wang, Y.-J. Yin, F. Wang, M. Li, J. Feng, H.-M. Zhang, J.-P. Zhang, S.-J. Liu, and W.-R. Chang Crystal Structures and Site-directed Mutagenesis of a Mycothiol-dependent Enzyme Reveal a Novel Folding and Molecular Basis for Mycothiol-mediated Maleylpyruvate Isomerization J. Biol. Chem., June 1, 2007; 282(22): 16288 - 15294. [Abstract] [Full Text] [PDF]
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M. J. Baumann, J. M. Eklof, G. Michel, A. M. Kallas, T. T. Teeri, M. Czjzek, and H. Brumer III Structural Evidence for the Evolution of Xyloglucanase Activity from Xyloglucan Endo-Transglycosylases: Biological Implications for Cell Wall Metabolism PLANT CELL, June 1, 2007; 19(6): 1947 - 1963. [Abstract] [Full Text] [PDF]
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E. J.M. Van Damme, R. Culerrier, A. Barre, R. Alvarez, P. Rouge, and W. J. Peumans A Novel Family of Lectins Evolutionarily Related to Class V Chitinases: An Example of Neofunctionalization in Legumes Plant Physiology, June 1, 2007; 144(2): 662 - 672. [Abstract] [Full Text] [PDF]
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A. A. McCarthy and J. G. McCarthy The Structure of Two N-Methyltransferases from the Caffeine Biosynthetic Pathway Plant Physiology, June 1, 2007; 144(2): 879 - 889. [Abstract] [Full Text] [PDF]
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J. Fan, Q. Liu, Q. Hao, M. Teng, and L. Niu Crystal Structure of Uroporphyrinogen Decarboxylase from Bacillus subtilis J. Bacteriol., May 1, 2007; 189(9): 3573 - 3580. [Abstract] [Full Text] [PDF]
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M. Nishimoto, S. Fushinobu, A. Miyanaga, M. Kitaoka, and K. Hayashi Molecular Anatomy of the Alkaliphilic Xylanase from Bacillus halodurans C-125 J. Biochem., May 1, 2007; 141(5): 709 - 717. [Abstract] [Full Text] [PDF]
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C.-L. Hung, J.-H. Liu, W.-C. Chiu, S.-W. Huang, J.-K. Hwang, and W.-C. Wang Crystal Structure of Helicobacter pylori Formamidase AmiF Reveals a Cysteine-Glutamate-Lysine Catalytic Triad J. Biol. Chem., April 20, 2007; 282(16): 12220 - 12229. [Abstract] [Full Text] [PDF]
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J. Li, M. Machius, J. L. Chuang, R. M. Wynn, and D. T. Chuang The Two Active Sites in Human Branched-chain {alpha}-Keto Acid Dehydrogenase Operate Independently without an Obligatory Alternating-site Mechanism J. Biol. Chem., April 20, 2007; 282(16): 11904 - 11913. [Abstract] [Full Text] [PDF]
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I. Alexeev, A. Sultana, P. Mantsala, J. Niemi, and G. Schneider Aclacinomycin oxidoreductase (AknOx) from the biosynthetic pathway of the antibiotic aclacinomycin is an unusual flavoenzyme with a dual active site PNAS, April 10, 2007; 104(15): 6170 - 6175. [Abstract] [Full Text] [PDF]
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J.-W. Nam and T. J. Kappock Cloning and transcriptional analysis of Crepis alpina fatty acid desaturases affecting the biosynthesis of crepenynic acid J. Exp. Bot., April 1, 2007; 58(6): 1421 - 1432. [Abstract] [Full Text] [PDF]
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