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Baxevanis AD 《Nucleic acids research》2003,31(1):1-12
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists' attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the jumping-off point from which to find specialized databases that may be of use in advancing biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries and updates for each of the databases included in this Collection are available through the Nucleic Acids Research Web site at http://nar.oupjournals.org. 相似文献
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Baxevanis AD 《Nucleic acids research》2001,29(1):1-10
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists' attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the initial point from which to find specialized databases that may be of use in biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries of each of the databases included in the Collection are available through the Nucleic Acids Research Web site, at http://www. nar.oupjournals.org. 相似文献
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Andreas D. Baxevanis 《Nucleic acids research》2002,30(1):1-12
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the initial point from which to find specialized databases that may be of use in biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries and updates for each of the databases included in the Collection are available through the Nucleic Acids Research Web site at http://nar.oupjournals.org. 相似文献
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A comprehensive DNA analysis computer program was described in the second special issue of Nucleic Acids Research on the applications of computers to research on nucleic acids by Stone and Potter (1). Criteria used in designing the program were user friendliness, ability to handle large DNA sequences, low storage requirement, migratability to other computers and comprehensive analysis capability. The program has been used extensively in an industrial-research environment. This paper talks about improvements to that program. These improvements include testing for methylation blockage of restriction enzyme recognition sites, homology analysis, RNA folding analysis, integration of a large DNA database (GenBank), a site specific mutagenesis analysis, a protein database and protein searching programs. The original design of the DNA analysis program using a command executive from which any analytical programs can be called, has proven to be extremely versatile in integrating both developed and outside programs to the file management system employed. 相似文献
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Bioinformatic Characterization of P-Type ATPases Encoded Within the Fully Sequenced Genomes of 26 Eukaryotes 总被引:1,自引:0,他引:1
P-type ATPases play essential roles in numerous processes, which in humans include nerve impulse propagation, relaxation of
muscle fibers, secretion and absorption in the kidney, acidification of the stomach and nutrient absorption in the intestine.
Published evidence suggests that uncharacterized families of P-type ATPases with novel specificities exist. In this study,
the fully sequenced genomes of 26 eukaryotes, including animals, plants, fungi and unicellular eukaryotes, were analyzed for
P-type ATPases. We report the organismal distributions, phylogenetic relationships, probable topologies and conserved motifs
of nine functionally characterized families and 13 uncharacterized families of these enzyme transporters. We have classified
these proteins according to the conventions of the functional and phylogenetic IUBMB-approved transporter classification system
(, Saier et al. in Nucleic Acids Res 34:181–186, 2006; Nucleic Acids Res 37:274–278, 2009).
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
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We introduce the PSSH ('Protein Sequence-to-Structure Homologies') database derived from HSSP2, an improved version of the HSSP ('Homology-derived Secondary Structure of Proteins') database [Dodge et al. (1998) Nucleic Acids Res., 26, 313-315]. Whereas each HSSP entry lists all protein sequences related to a given 3D structure, PSSH is the 'inverse', with each entry listing all structures related to a given sequence. In addition, we introduce two other derived databases: HSSPchain, in which each entry lists all sequences related to a given PDB chain, and HSSPalign, in which each entry gives details of one sequence aligned onto one PDB chain. This re-organization makes it easier to navigate from sequence to structure, and to map sequence features onto 3D structures. Currently (September 2002), PSSH provides structural information for over 400 000 protein sequences, covering 48% of SWALL and 61% of SWISS-PROT sequences; HSSPchain provides sequence information for over 25 000 PDB chains, and HSSPalign gives over 14 million sequence-to-structure alignments. The databases can be accessed via SRS 3D, an extension to the SRS system, at http://srs3d.ebi.ac.uk/. 相似文献
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A database comprising all ligand-binding sites of known structure aligned with all related protein sequences and structures is described. Currently, the database contains approximately 50000 ligand-binding sites for small molecules found in the Protein Data Bank (PDB). The structure-structure alignments are obtained by the Combinatorial Extension (CE) program (Shindyalov and Bourne, Protein Eng., 11, 739-747, 1998) and sequence-structure alignments are extracted from the ModBase database of comparative protein structure models for all known protein sequences (Sanchez et al., Nucleic Acids Res., 28, 250-253, 2000). It is possible to search for binding sites in LigBase by a variety of criteria. LigBase reports summarize ligand data including relevant structural information from the PDB file, such as ligand type and size, and contain links to all related protein sequences in the TrEMBL database. Residues in the binding sites are graphically depicted for comparison with other structurally defined family members. LigBase provides a resource for the analysis of families of related binding sites. 相似文献
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Laurent Falquet Marco Pagni Philipp Bucher Nicolas Hulo Christian J. A. Sigrist Kay Hofmann Amos Bairoch 《Nucleic acids research》2002,30(1):235-238
PROSITE [Bairoch and Bucher (1994) Nucleic Acids Res., 22, 3583–3589; Hofmann et al. (1999) Nucleic Acids Res., 27, 215–219] is a method of identifying the functions of uncharacterized proteins translated from genomic or cDNA sequences. The PROSITE database (http://www.expasy.org/prosite/) consists of biologically significant patterns and profiles designed in such a way that with appropriate computational tools it can rapidly and reliably help to determine to which known family of proteins (if any) a new sequence belongs, or which known domain(s) it contains. 相似文献
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Update of the viroid and viroid-like sequence database: addition of a hepatitis delta virus RNA section. 总被引:3,自引:1,他引:2
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Recently, we developed and made available an online database that includes all the reported (to our knowledge) viroid and viroid-like RNA sequences [Bussire,F., Lafontaine,D. and Perreault,J.-P. (1996)Nucleic Acids Res.24, 1793-1798]. We report here an update of this catalogue which includes the addition of a new section devoted to human hepatitis delta virus (vHDV) sequences. This new section comprises all available vHDV sequences, irrespective of their completeness, which have been either published or were available from nucleic acid libraries. Additional structural characteristics of the vHDV genome, such as the positions of the self-catalytic domains, the antigen open reading frames, etc., are also included. The catalogue is available on the World Wide Web (see text) in a user-friendly form. It should provide an excellent reference point for further molecular studies of these small circular pathogenic RNAs. 相似文献
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The factor VIII Structure and Mutation Resource Site: HAMSTeRS version 4. 总被引:14,自引:0,他引:14
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Since 1996 the HAMSTeRS (Haemophilia A Mutation, Search, Test and Resource Site) WWW site has provided an online resource for access to data on the molecular pathology of haemophilia A, replacing previous text editions of the Haemophilia A Database published in Nucleic Acids Research . This report describes the continued development of the site (version 4), and in particular the expansion of factor VIII (FVIII) structure-related features. Access to the mutation database itself, both for searching the listings and for submission of new mutations, is via custom-designed forms: more powerful Boolean searches of the point mutations in the database are also available. During 1997 a total of 22 novel missense mutations were reported, increasing the total number of unique variants now described to 252 (238 in exonic sequences and 14 at intronic splice junctions). Currently, a total of 586 individual reports with associated phenotypic data are available for searching by any category including phenotype. The FVIII structure section now includes a download of a FVIII A domain homology model in Protein Data Bank format and a multiple alignment of the FVIII amino-acid sequencies from four species (human, murine, porcine and canine) in addition to the virtual reality simulations, secondary structural data and FVIII animation already available. Finally, to aid navigation across this site, a clickable roadmap of the main features provides easy access to the page desired. Our intention is that continued development and updating of the site shall provide workers in the fields of molecular and structural biology with a one-stop resource site to facilitate FVIII research and education. The HAMSTeRS URL is http://europium.mrc.rpms.ac.uk 相似文献
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L R Ceci M Volpicella S Liuni V Volpetti F Licciulli R Gallerani 《Nucleic acids research》1999,27(1):156-157
The PLMItRNA database contains information and multialignments of tRNA genes and molecules detected in higher plant mitochondria. It has been developed from a previous compilation of higher plant mitochondrial tRNA genes [Sagliano,A., Volpicella,M., Gallerani,R. and Ceci,L.R. (1998) Nucleic Acids Res., 26, 154-155] and implemented with data and sequences of tRNA molecules retrieved from the literature. The current version of the database reports information on 171 genes and 16 tRNA molecules from 24 plants. PLMItRNA is accessible via WWW at http://bio-www.ba.cnr.it:8000/srs/ 相似文献
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《Phytochemical analysis : PCA》2003,14(1):60-66
In order to keep subscribers up-to-date with the latest developments in their field, John Wiley &Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of phytochemical analysis. Each bibliography is divided into 13 sections: 1 Books, Reviews &Symposia; 2 General; 3 Nucleic Acids; 4 Amino Acids, Proteins &Enzymes; 5 Carbohydrates; 6 Lipids; 7 Secondary Products; 8 Growth Regulators; 9 Industrially-Important Products; 10 Toxins/Allergens; 11 Pigments; 12 Vitamins; 13 Others. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. 相似文献
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de Bakker PI Bateman A Burke DF Miguel RN Mizuguchi K Shi J Shirai H Blundell TL 《Bioinformatics (Oxford, England)》2001,17(8):748-749
summary: We describe an extension to the Homologous Structure Alignment Database (HOMSTRAD; Mizuguchi et al., Protein Sci., 7, 2469-2471, 1998a) to include homologous sequences derived from the protein families database Pfam (Bateman et al., Nucleic Acids Res., 28, 263-266, 2000). HOMSTRAD is integrated with the server FUGUE (Shi et al., submitted, 2001) for recognition and alignment of homologues, benefitting from the combination of abundant sequence information and accurate structure-based alignments. AVAILABILITY The HOMSTRAD database is available at: http://www-cryst.bioc.cam.ac.uk/homstrad/. Query sequences can be submitted to the homology recognition/alignment server FUGUE at: http://www-cryst.bioc.cam.ac.uk/fugue/. 相似文献
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《Phytochemical analysis : PCA》2004,15(3):204-211
In order to keep subscribers up‐to‐date with the latest developments in their field, John Wiley &Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of phytochemical analysis. Each bibliography is divided into 13 sections: 1 Books, Reviews &Symposia; 2 General; 3 Nucleic Acids; 4 Amino Acids, Proteins &Enzymes; 5 Carbohydrates; 6 Lipids; 7 Secondary Products; 8 Growth Regulators; 9 Industrially‐Important Products; 10 Toxins/Allergens; 11 Pigments; 12 Vitamins; 13 Others. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. 相似文献
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《Phytochemical analysis : PCA》2006,17(1):63-70
In order to keep subscribers up‐to‐date with the latest developments in their field, John Wiley &Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of phytochemical analysis. Each bibliography is divided into 13 sections: 1 Books, Reviews &Symposia; 2 General; 3 Nucleic Acids; 4 Amino Acids, Proteins &Enzymes; 5 Carbohydrates; 6 Lipids; 7 Secondary Products; 8 Growth Regulators; 9 Industrially‐Important Products; 10 Toxins/Allergens; 11 Pigments; 12 Vitamins; 13 Others. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. 相似文献