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tny's library [310 articles]

最近录入 tny's 文献库:按阅读优先等级排序.
  • Functional cartography of complex metabolic networks
    Nature, Vol. 433, No. 7028. (24 February 2005), pp. 895-900.
    by Roger Guimera, LAN Luis
    posted to enzyme network by tny on 2006-04-07 12:02:55 as *** along with 14 people and 4 groups carlk camster dbk BioGeek Borelli lfriedl balajis alexg eweaver wnpx cjeans kdang RobMills Diego_Prada streptomyces dbk-lab kdl Bioinformatics
  • Modules, multidomain proteins and organismic complexity
    FEBS Journal, Vol. 272, No. 19., pp. 5064-5078.
    posted to domain journal_club protein by tny on 2005-12-07 09:27:21 as ***
  • Evolution of function in protein superfamilies, from a structural perspective
    Journal of Molecular Biology, Vol. 307, No. 4. (6 April 2001), pp. 1113-1143.
    by Annabel E Todd, Christine A Orengo, Janet M Thornton
    posted to 12dec05 enzyme protein by tny on 2005-12-07 07:01:36 as *** along with 8 people and 2 groups sim82 ana kuhn chad_davis sriram_s choonpeng cdallett uz_labu_laimi structural_bioinformatics Bioinformatics
  • Catalysing New Reactions during Evolution: Economy of Residues and Mechanism
    Journal of Molecular Biology, Vol. 331, No. 4. (22 August 2003), pp. 829-860.
    by Gail J Bartlett, Neera Borkakoti, Janet M Thornton
    posted to 13jan06 catalytic enzyme protein by tny on 2005-12-07 05:23:00 as ***
  • Understanding nature's catalytic toolkit.
    Trends Biochem Sci (5 October 2005)
    by Alex Gutteridge, Janet M M Thornton
    posted to 12dec05 enzyme protein review by tny on 2005-12-05 14:07:57 as *** along with 10 people and 4 groups sim82 ana jwm Einat alexg gbart eweaver noby siebertm grottenolm structural_bioinformatics Radiation_Damage Stressosome Bioinformatics
  • Analysis of Catalytic Residues in Enzyme Active Sites
    Journal of Molecular Biology, Vol. 324, No. 1. (15 November 2002), pp. 105-121.
    by Gail J Bartlett, Craig T Porter, Neera Borkakoti, Janet M Thornton
    posted to catalytic enzyme protein by tny on 2005-11-30 09:38:17 as *** along with 2 people baaden chrn
  • Differences in evolutionary pressure acting within highly conserved ortholog groups
    BMC Evolutionary Biology, Vol. 8 (17 July 2008), 208.
    by Teresa M Przytycka, Raja Jothi, L Aravind, David J Lipman
    posted to ortholog evolutionary_rate entropy_profile by tny on 2008-07-24 10:17:12 as **
  • Phylogenetic analyses suggest multiple changes of substrate specificity within the Glycosyl hydrolase 20 family
    BMC Evolutionary Biology, Vol. 8 (22 July 2008), 214.
    by Jari Intra, Giulio Pavesi, David S Horner
    posted to evolution enzyme_function by tny on 2008-07-24 10:09:00 as **
  • LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions
    Protein Eng., Vol. 8, No. 2. (1 February 1995), pp. 127-134.
    by Andrew C Wallace, Roman A Laskowski, Janet M Thornton
    posted to ligand_binding database_issue by tny on 2008-07-22 02:47:06 as **
  • Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages — PNAS
    posted to tyrosinekinase evolution enzyme_superfamily domain_combination by tny on 2008-07-16 06:34:13 as **
  • Golgi α-mannosidase II cleaves two sugars sequentially in the same catalytic site
    e Proceedings of the National Academy of Sciences (2008)
    by Niket Shah, Douglas A Kuntz, David R Rose
    posted to sugar_binding multifunctional_enzyme enzyme_structure catalytic_site by tny on 2008-07-16 06:21:33 as **
  • The new higher level classification of eukaryotes with emphasis on the taxonomy of protists.
    J Eukaryot Microbiol, Vol. 52, No. 5. (t 2005), pp. 399-451.
    by SM Adl, AG Simpson, MA Farmer, RA Andersen, OR Anderson, JR Barta, SS Bowser, G Brugerolle, RA Fensome, S Fredericq, TY James, S Karpov, P Kugrens, J Krug, CE Lane, LA Lewis, J Lodge, DH Lynn, DG Mann, RM McCourt, L Mendoza, O Moestrup, SE Mozley-Standridge, TA Nerad, CA Shearer, AV Smirnov, FW Spiegel, MF Taylor
    posted to phylogeny by tny on 2008-07-11 10:01:58 as ** along with 4 people and 1 group jmeppley jdelcampo Fabnot cmzmasek Microbial-Ecology
  • Of clades and clans: terms for phylogenetic relationships in unrooted trees
    Trends in Ecology & Evolution, Vol. 22, No. 3. (March 2007), pp. 114-115.
    by Mark Wilkinson, James O Mcinerney, Robert P Hirt, Peter G Foster, Martin T Embley
    posted to review phylogeny by tny on 2008-07-11 03:26:51 as ** along with 4 people and 2 groups dchughes echinotrix agg19954 TaqSys G4ID Genetics-of-Gambling
  • A short history of the thermodynamics of enzyme-catalyzed reactions.
    J Biol Chem, Vol. 279, No. 27. (2 July 2004), pp. 27831-27836.
    by RA Alberty
    posted to thermodynamics review enzyme by tny on 2008-06-25 04:45:37 as ** along with 2 people proportional robert
  • Tryptophan synthase: A multienzyme complex with an intramolecular tunnel
    The Chemical Record, Vol. 1, No. 2. (2001), pp. 140-151.
    by Edith W Miles
    posted to multifunctional_enzyme by tny on 2008-06-23 09:32:59 as **
  • Interdomain interactions in oligomeric enzymes: creation of asymmetry in homo-oligomers and role in metabolite channeling between active centers of hetero-oligomers
    FEBS Letters, Vol. 487, No. 3. (5 January 2001), pp. 327-332.
    by Natalya K Nagradova
    posted to multifunctional_enzyme by tny on 2008-06-23 09:29:17 as **
  • Hierarchical structure and the prediction of missing links in networks
    Nature, Vol. 453, No. 7191., pp. 98-101.
    by Aaron Clauset, Cristopher Moore, MEJ Newman
    posted to network hierarchy by tny on 2008-05-02 08:09:11 as ** along with 35 people sen_cheng jjray rds Borelli ptrobajo apwesolowski dpf cmmorel fbaroni balicea cmor kengg pbull jago Ema gtgt15 hryk nedwards i-stevenson pinney elsantosneto markusd eyliu craigwilson06 jyuh margaritis gagliol bryanhughes akshat tmmurali cactus AbnerCYH briordan deanmalmgren soramame_0518
  • Error bars in experimental biology
    J. Cell Biol., Vol. 177, No. 1. (9 April 2007), pp. 7-11.
    by Geoff Cumming, Fiona Fidler, David L Vaux
    posted to statistics by tny on 2008-02-18 02:33:39 as ** along with 32 people and 5 groups mjoach arindrartow jyuh brian ana batallah manduca kuhn Borelli dayjm kristina chad_davis dullhunk rabu lechristophe nelmor jdelcampo fishtank emmahe lisa1 Daria_G devender bmaust cabbagezs natstreet winterschlaefer krokicki loopback007 wilbur tdmckee renatomilani delenca structural_bioinformatics Bioinformatics VisionLab FlowCytometry Microbial-Ecology
  • Relating three-dimensional structures to protein networks provides evolutionary insights.
    Science, Vol. 314, No. 5807. (22 December 2006), pp. 1938-1941.
    by PM Kim, LJ Lu, Y Xia, MB Gerstein
    posted to network structure by tny on 2008-02-15 03:11:29 as ** along with 17 people and 2 groups carlk saket paolomarcatili bicko lfriedl chad_davis Einat choonpeng timflutre grahamc ramensky massivemayhem efge lpfernandes cdeane Pao-Yang phoenixzxl structural_bioinformatics kdl
  • Alignment Uncertainty and Genomic Analysis
    Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476.
    by Karen M Wong, Marc A Suchard, John P Huelsenbeck
    posted to alignment tree_comparison by tny on 2008-02-04 10:32:24 as ** along with 24 people and 2 groups bpcusack pradiptaray jdelcampo timflutre gracio adacier jyuh bpb aprasad dayjm dpollard djkt cjeans zwang lisa1 cactus biomcgary lilou kinestetika dandaman gjuggler renatomilani mclarenv youdon EisenLab microbiology_nijmegen
  • Power laws, Pareto distributions and Zipf's law
    Contemporary Physics, Vol. 46, No. 5. (September 2005), pp. 323-351.
    by Mej Newman
    posted to power_low scale_free by tny on 2008-02-03 10:22:02 as ** along with 7 people and 2 groups mapio itmeson muraken simba06 dbatorski dbilar dberreby dalab_dsi CARTOON
  • STRUCTURE, DYNAMICS, AND CATALYTIC FUNCTION OF DIHYDROFOLATE REDUCTASE
    Annual Review of Biophysics and Biomolecular Structure, Vol. 33, No. 1. (2004), 119.
    by Jason
    posted to catalysis enzyme by tny on 2008-02-01 10:41:54 as **
  • Rhodobacter capsulatus OlsA Is a Bifunctional Enyzme Active in both Ornithine Lipid and Phosphatidic Acid Biosynthesis
    J. Bacteriol., Vol. 189, No. 23. (1 December 2007), pp. 8564-8574.
    by Semra Aygun-Sunar, Rahmi Bilaloglu, Howard Goldfine, Fevzi Daldal
    posted to enzyme multifunctional_enzyme by tny on 2008-02-01 10:39:16 as **
  • Defining functional distances over Gene Ontology
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Angela D Pozo, Florencio Pazos, Alfonso Valencia
    posted to no-tag by tny on 2008-01-30 14:36:09 as ** along with 5 people and 2 groups carlk barry grahamc sobolevnrm barriot Bioinformatics baker-group
  • Understanding the molecular machinery of genetics through 3D structures
    Nature Reviews Genetics
    by JM Thornton, Laskowski
    posted to genetics structure by tny on 2008-01-08 03:45:43 as **
  • Evolutionary history and functional implications of protein domains and their combinations in eukaryotes
    Genome Biology, Vol. 8 (25 June 2007), R121.
    by Masumi Itoh, Jose C Nacher, Kei-Ichi Kuma, Susumu Goto, Minoru Kanehisa
    posted to domain_combination eukaryote evolution by tny on 2007-12-27 04:48:51 as ** along with 2 people cjeans dandaman
  • Genetic variation in the cysteine biosynthesis pathway causes sensitivity to pharmacological compounds
    Proceedings of the National Academy of Sciences, Vol. 104, No. 49. (4 December 2007), pp. 19387-19391.
    by Hyun S Kim, Justin C Fay
    posted to enzyme_function experiment pathway by tny on 2007-12-07 03:50:00 as ** along with 1 person dbensasson
  • Biochemical and Structural Characterization of a Novel Family of Cystathionine [beta]-Synthase Domain Proteins Fused to a Zn Ribbon-Like Domain
    Journal of Molecular Biology, Vol. 375, No. 1. (4 January 2008), pp. 301-315.
    by Michael Proudfoot, Stephen A Sanders, Alex Singer, Rongguang Zhang, Greg Brown, Andrew Binkowski, Linda Xu, Jonathan A Lukin, Alexey G Murzin, Andrzej Joachimiak, Cheryl H Arrowsmith, Aled M Edwards, Alexei V Savchenko, Alexander F Yakunin
    posted to enzyme metal_binding by tny on 2007-12-04 03:36:40 as **
  • Divergence of Cofactor Recognition across Evolution: Coenzyme A Binding in a Prokaryotic Arylamine N-Acetyltransferase
    Journal of Molecular Biology, Vol. 375, No. 1. (4 January 2008), pp. 178-191.
    by Elizabeth Fullam, Isaac M Westwood, Matthew C Anderton, Edward D Lowe, Edith Sim, Martin E Noble
    posted to enzyme enzyme_superfamily evolution by tny on 2007-12-04 03:25:10 as ** along with 1 person dkanter
  • Evolution of binding sites for zinc and calcium ions playing structural roles
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by James W Torrance, Malcolm W Macarthur, Janet M Thornton
    posted to metal_binding by tny on 2007-12-04 03:19:56 as ** along with 2 people jwm grottenolm
  • Increased Catalytic Efficiency following Gene Fusion of Bifunctional Methionine Sulfoxide Reductase Enzymes from Shewanella oneidensis
    Biochemistry (13 November 2007)
    by B Chen, LM Markillie, Y Xiong, MU Mayer, TC Squier
    posted to experiment multifunctional_enzyme by tny on 2007-11-19 05:37:45 as **
  • History of the enzyme nomenclature system
    Bioinformatics, Vol. 16, No. 1. (1 January 2000), pp. 34-40.
    by Keith Tipton, Sinead Boyce
    posted to enzyme review by tny on 2007-10-10 13:32:30 as ** along with 2 people and 1 group jxl robert EC
  • Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA)
    Journal of Molecular Evolution
    by Juan AG Ranea, Antonio Sillero, Janet M Thornton, Christine A Orengo
    posted to evolution luca protein by tny on 2007-10-09 12:16:42 as ** along with 4 people and 2 groups jwm ana barry grottenolm structural_bioinformatics Bioinformatics
  • Genome-wide analysis of enzyme structure-function combination across three domains of life.
    Protein Pept Lett, Vol. 14, No. 3. (2007), pp. 291-297.
    by Z Zhang, YR Tang
    posted to enzyme_function enzyme_structure scopec by tny on 2007-10-05 13:39:56 as **
  • Domain Architecture of Pyruvate Carboxylase, a Biotin-Dependent Multifunctional Enzyme
    Science, Vol. 317, No. 5841. (24 August 2007), pp. 1076-1079.
    by Martin S Maurice, Laurie Reinhardt, Kathy H Surinya, Paul V Attwood, John C Wallace, Wallace W Cleland, Ivan Rayment
    posted to multifunctional_enzyme structure by tny on 2007-10-05 12:52:02 as ** along with 1 person grottenolm
  • TOPD/FMTS: a new software to compare phylogenetic trees
    Bioinformatics, Vol. 23, No. 12. (15 June 2007), pp. 1556-1558.
    by Pere Puigbo, Santiago Garcia-Vallve, James O Mcinerney
    posted to tree_comparison by tny on 2007-09-25 11:55:18 as **
  • The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case
    BMC Evolutionary Biology, Vol. 7, No. Suppl 2. (2007)
    by Renato Fani, Matteo Brilli, Marco Fondi, Pietro Lio
    posted to enzyme evolution gene_fusion his_metabolism by tny on 2007-09-18 03:52:04 as **
  • Natural history and evolutionary principles of gene duplication in fungi
    Nature, Vol. 449, No. 7158., pp. 54-61.
    by Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev
    posted to gene_fusion yea by tny on 2007-09-10 07:56:07 as ** along with 11 people and 4 groups pkm aheilbut dpollard dchughes djkt stajich zwang biomcgary lp2 tzhughes maximilianh EisenLab G4ID Genetics-of-Gambling Berkeley Mycology
  • Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon
    Journal of Molecular Biology, Vol. 372, No. 3. (21 September 2007), pp. 817-845.
    by Pier F Gherardini, Mark N Wass, Manuela Helmer-Citterich, Michael J Sternberg
    posted to convergent enzyme evolution by tny on 2007-09-04 06:45:08 as ** along with 6 people and 2 groups sim82 barry tjimenez jjray chad_davis Minty structural_bioinformatics Bioinformatics
  • RadCon: phylogenetic tree comparison and consensus
    Bioinformatics, Vol. 16, No. 5. (1 May 2000), pp. 486-487.
    by Joseph L Thorley, Roderic D Page
    posted to evolution tool by tny on 2007-07-04 10:45:34 as ** along with 1 person aprasad
  • The Classification and Origins of Protein Folding Patterns - Annual Review of Biochemistry, 59(1):1007 - First Page Image
    posted to unread by tny on 2007-07-04 09:28:05 as **
  • PROTEIN FOLDS IN THE ALL- AND ALL- CLASSES -
    Annual Review of Biophysics and Biomolecular Structure
    by C Chothia
    posted to unread by tny on 2007-07-02 12:47:45 as **
  • Universal Sharing Patterns in Proteomes and Evolution of Protein Fold Architecture and Life
    Journal of Molecular Evolution, Vol. 60, No. 4. (1 April 2005), pp. 484-498.
    by Gustavo Caetano-Anollés, Derek Caetano-Anollés
    posted to enzyme evolution by tny on 2007-07-02 11:27:38 as **
  • MANET: tracing evolution of protein architecture in metabolic networks
    BMC Bioinformatics, Vol. 7 (19 July 2006), 351.
    by Hee S Kim, Jay E Mittenthal, Gustavo Caetano-Anolles
    posted to database_issue enzyme phylogeny by tny on 2007-07-02 11:17:24 as ** along with 2 people kuhn balajis
  • GENOME TREES AND THE NATURE OF GENOME EVOLUTION
    Annual Review of Microbiology
    posted to evolution tree unread by tny on 2007-07-02 11:15:12 as **
  • Stability for Function Trade-Offs in the Enolase Superfamily "Catalytic Module"
    by Pc Babbit
    posted to enzyme by tny on 2007-06-28 14:37:50 as **
  • The Identification of Similarities between Biological Networks: Application to the Metabolome and Interactome
    Journal of Molecular Biology, Vol. 369, No. 4. (15 June 2007), pp. 1126-1139.
    by Adrian P Cootes, Stephen H Muggleton, Michael J Sternberg
    posted to interactome metabolome network by tny on 2007-05-22 09:55:10 as **
  • Occurrence of multiple, independent gene fusion events for the fifth and sixth enzymes of pyrimidine biosynthesis in different eukaryotic groups
    Gene, Vol. 394, No. 1-2. (1 June 2007), pp. 78-86.
    by Takashi Makiuchi, Takeshi Nara, Takeshi Annoura, Tetsuo Hashimoto, Takashi Aoki
    posted to gene_fusion multifunctional_enzyme by tny on 2007-05-15 10:30:23 as **
  • Construction of the bifunctional enzyme cellulase-β-glucosidase from the hyperthermophilic bacterium Thermotoga maritima
    Biotechnology Letters, Vol. 29, No. 6. (21 June 2007), pp. 931-936.
    by Su-Young Hong, Jin-Suk Lee, Kye-Man Cho, Renukaradhya Math, Yong-Hee Kim, Sun-Joo Hong, Yong-Un Cho, Soo-Jeong Cho, Hoon Kim, Han-Dae Yun
    posted to gene_fusion multifunctional_enzyme by tny on 2007-05-15 10:29:55 as **
  • Mass spectrometry and the search for moonlighting proteins.
    Mass Spectrom Rev, Vol. 24, No. 6. (c 2005), pp. 772-782.
    by CJ Jeffery
    posted to enzyme moonlighting_enzyme by tny on 2007-04-16 03:34:42 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
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