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1
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85030360232
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The EMBL nucleotide sequence database on the World Wide Web at URL: http://www.ebi.ac.uk_docs/embl_db/ebi/topembl.html
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2
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85030363917
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DNA Data Bank of Japan on the World Wide Web at URL: http://www.ddbj.nig.ac.jp/
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3
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85030363886
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Entrez genomes on the World Wide Web at URL: http://www.ncbi.nlm.nih.gov/Entrez/Genome/org.html
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4
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85030366014
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GenomeNet WWW server on the World Wide Web at URL: http://www.genome.ad.jp/
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5
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85030366917
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The Sanger Centre Projects on the World Wide Web at URL: http://www.sanger.ac.uk/Projects/
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6
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85030363630
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The Institute for Genomic Research on the World Wide Web at URL: http://www.tigr.org/
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7
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85030370116
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The University of Oklahoma's Advanced Center for Genome Technology on the World Wide Web at URL: http://www.genome.ou.edu/
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8
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85030369608
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Completed and ongoing genome projects monitor on the World Wide Web at URL: http://geta.life.uiuc.edu/-nikos/genomes.html
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9
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85030364441
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Genomic databases on the Internet on the World Wide Web at URL: http://bmbsgi12.leeds.ac.uk/bmbknd/DNA/genomic.html
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10
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85030370128
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Annotated links to Biochemistry and Molecular Biology Internet resources on the World Wide Web at URL: http://www.sgi.bls.umkc.edu/biolinks/
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11
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85030365931
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The SwissProt data library is the best annotated protein sequence library that is used to predict protein functions. Please note that it is not infallible!
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ExPASy Molecular Biology Server on the World Wide Web at URL: http://expasy.hcuge.ch/www/expasy-top.html The SwissProt data library is the best annotated protein sequence library that is used to predict protein functions. Please note that it is not infallible!
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12
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85030366334
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The Brookhaven National Laboratory Protein Data Bank on the World Wide Web at URL: http://www.pdb.bnl.gov/pdb-docs/index.html
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F1-ATPase is a highly efficient molecular motor that rotates with discrete 120 degree steps
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This beautiful experimental work demonstrates that ATP synthase is the smallest engine in the world
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This article, together with [33], provides a dictionary of folds and enables them to be connected with sequence multi-alignments
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The GAIA software illustrates a recent case of the general tendency to develop multipurpose engines for semi-automatic genome annotation (e.g. Imagene), in contrast to automatic annotation (e.g. Genotator, Genequiz and so on)
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Pac Symp Biocomput
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Overton, G.C.1
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A further reflection after MAGPIE, which set the stage for an integrated view of genome annotation. MAGPIE was an important step forward that permitted the community of genome annotators to discover the impossibility, in the absence of entirely new concepts, of managing the huge amount of data generated by genome comparisons
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Gaasterland T, Ragan MA: Constructing multigenome views of whole microbial genomes. Microb Comp Genomics 1998, 3:177-192. A further reflection after MAGPIE, which set the stage for an integrated view of genome annotation. MAGPIE was an important step forward that permitted the community of genome annotators to discover the impossibility, in the absence of entirely new concepts, of managing the huge amount of data generated by genome comparisons.
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Microb Comp Genomics
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A standard, but useful, automatic construction of the multi-alignment of protein domains
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Corpet F, Gouzy J, Kahn D: Recent improvements of the ProDom database of protein domain families. Nucleic Acids Res 1999, 27:263-267. A standard, but useful, automatic construction of the multi-alignment of protein domains.
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An interesting illustration of the combination of phylogenetic, biochemical and sequence data in order to understand the formation of multidomain proteins
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A remarkable synthesis of a cork-in-a-bottleneck pore structure. FhuA is located in the outer membrane of E. coli and one might have expected a static structure, like that of the porins. This work illustrates how a signal from the inside of the cell, mediated by TonB through the periplasm, might induce an allosteric transition moving the cork and allowing the iron-carrying siderophore to pass through FhuA
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Ferguson AD, Hofmann E, Coulton JW, Diederichs K, Welte W: Siderophore-mediated iron transport: Crystal structure of FhuA with bound lipopolysaccharide. Science 1998, 282:2215-2226. A remarkable synthesis of a cork-in-a-bottleneck pore structure. FhuA is located in the outer membrane of E. coli and one might have expected a static structure, like that of the porins. This work illustrates how a signal from the inside of the cell, mediated by TonB through the periplasm, might induce an allosteric transition moving the cork and allowing the iron-carrying siderophore to pass through FhuA.
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Science
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The complete genome sequence of the gram positive model organism Bacillus subtilis (strain 168)
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The long-awaited structure of the ATP-binding subunit of an ABC transporter, raising many new questions
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The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases
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Resolving the ribosome protein L25 structure illustrates the power of the new NMR techniques. It also raises major questions about the origin and fate of RNA-binding proteins. What are the similarities among sequences with a structure in common and do they display common functions?
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Stoldt M, Wohnert J, Gorlach M, Brown LR: The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases. EMBO J 1998, 17:6377-6384. Resolving the ribosome protein L25 structure illustrates the power of the new NMR techniques. It also raises major questions about the origin and fate of RNA-binding proteins. What are the similarities among sequences with a structure in common and do they display common functions?
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A very controversial view on the first cells found at the origin of life. Using sequence data correlated to the corresponding functions, Gupta reverts to the prokaryote/eukaryote dichotomy, proposing that Gram-positive eubacteria and archaebacteria form the original class (monoderms) and that Gram-negative eubacteria (diderms) engulfed an archaebacterial type to form the eukaryotic lineage
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Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein
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Schindelin H, Marahiel MA, Heinemann U: Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein. Nature 1993, 364:164-168.
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Crystal structures of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 å resolution
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An important protein containing hypusine, an unusual amino acid, is described (see, also, [57])
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Kim KK, Hung LW, Yokota H, Kim R, Kim SH: Crystal structures of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 å resolution. Proc Natl Acad Sci USA 1998, 95:10419-10424. An important protein containing hypusine, an unusual amino acid, is described (see, also, [57]).
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Proc Natl Acad Sci USA
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Kim, K.K.1
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Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 å resolution
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Peat TS, Newman J, Waldo GS, Berendzen J, Terwilliger TC: Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 å resolution. Structure 1998, 6:1207-1214.
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RNA binding strategies of ribosomal proteins
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Draper DE, Reynaldo LP: RNA binding strategies of ribosomal proteins. Nucleic Acids Res 1999, 27:381-388.
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Adenylyl cyclases: A heterogeneous class of ATP-utilizing enzymes
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Barzu O, Danchin A: Adenylyl cyclases: A heterogeneous class of ATP-utilizing enzymes. Prog Nucleic Acid Res Mol Biol 1994, 49:241-283.
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Structure of the adenylyl cyclase catalytic core
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[Published erratum appears in Nature 1997, 388:204.]
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Zhang G, Liu Y, Ruoho AE, Hurley JH: Structure of the adenylyl cyclase catalytic core. Nature 1997, 386:247-253. [Published erratum appears in Nature 1997, 388:204.]
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Zhang, G.1
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61
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Crystal structure of the catalytic domains of adenylyl cyclase in a complex with GsαGTPγS
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Tesmer JJ, Sunahara RK, Gilman AG, Sprang SR: Crystal structure of the catalytic domains of adenylyl cyclase in a complex with GsαGTPγS. Science 1997, 278:1907-1916.
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Indigo: A world-wide-web review of genomes and gene functions
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The concept of 'neighborhood' is illustrated in this review, showing how to use an inductive approach to understand, knowing its sequence, the function of a protein
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Nitschké P, Guerdoux-Jamet P, Chiapello H, Faroux G, Hénaut C, Hénaut A, Danchin A: Indigo: A world-wide-web review of genomes and gene functions. FEMS Microbiol Rev 1998, 22:207-227. The concept of 'neighborhood' is illustrated in this review, showing how to use an inductive approach to understand, knowing its sequence, the function of a protein.
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FEMS Microbiol Rev
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Nitschké, P.1
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Danchin, A.7
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High-resolution protein design with backbone freedom
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This paper looks towards the future of protein design
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Harbury PB, Plecs JJ, Tidor B, Alber T, Kim PS: High-resolution protein design with backbone freedom. Science 1998, 282:1462-1467. This paper looks towards the future of protein design.
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Science
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Harbury, P.B.1
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