- Email: [email protected]
Nucleic acids
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Nucleic acids Sequences and topology Web alert Judith Murray-Rust*, Jeremy H Lakey† and Eric D Scheeff‡ A selection of World Wide Web sites relevant to reviews published in this issue of Current Opinion in Structural Biology. Addresses *Crystallography Department, Birkbeck College, London WC1E 7HX, UK; e-mail: [email protected] † Laboratoire de Chimie Physique des Polymeres et Membranes, Ecole Polytechnique Federale de Lausanne, Switzerland; e-mail: [email protected] ‡ San Diego Supercomputing Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA; e-mail: [email protected] Current Opinion in Structural Biology 2000, 10:273–274
Nucleic acids Access Excellence Graphics Gallery http://www.accessexcellence.org/AB/GG/ The Access Excellence site, run by the National Health Museum, USA, offers a range of resources aimed at teachers in the biomedical area. The graphics gallery highlighted here not only has some excellent images of nucleic acid biochemistry, but also contains graphics that describe cell division, metabolism, viruses and so on. The nucleic acids section describes the Herschey–Chase experiment, the central dogma of molecular biology and models of DNA replication, to name but a few. Molecular Expressions Photo Gallery: The DNA Collection http://micro.magnet.fsu.edu/micro/gallery/dna/dna.html This is one of the pages from the Photo Gallery of the Molecular Expressions web site, which features many pages describing the world of optics and microscopy. Here, the use of polarised light microscopy enables pictures of the crystalline structure of DNA to be colourfully demonstrated. This makes a change from the over-used double helix! The New PovChem Homepage http://www.chemicalgraphics.com/PovChem/ This is the homepage of PovChem, a program that turns Protein Data Bank (PDB) files into input suitable for ray tracing with the POV-Ray program to produce high-quality images at any resolution. The results for DNA are presented here and a download facility for the software is available. The NDB Atlas of Nucleic Acid Structures http://ndbserver.rutgers.edu/NDB/NDBATLAS/index.html The Biological Structure Resource for the Nucleic Acid Database is maintained at Rutgers University, USA, with mirror sites worldwide. Among its several services, the database provides this compendium of the available nucleic acid structures, including protein–DNA and protein–RNA complexes, with full crystallographic descriptions.
Molecular Dynamics Simulations of the Glucocorticoid Receptor http://www.msi.umn.edu/Projects/mg90601/jbmsd1.html The full title is “Molecular dynamics simulations in solvent of the glucocorticoid receptor protein in complex with a glucocorticoid response element DNA sequence”. This is a web version of a paper previously published in the Journal of Biomolecular Structure and Dynamics by Harris et al. from the Abbott Northwestern Hospital Cancer Research Laboratory, Minneapolis. The figures contain JPEG movies of the dynamics of the nucleic acid and protein computed in solvent. The Comparative RNA Web Site http://www.rna.icmb.utexas.edu/ Robin R Gutell’s group at the University of Texas at Austin (Institute for Cellular and Molecular Biology) has recently established this RNA site, which includes a discussion on methods of structure prediction and methods of comparative sequence analysis, a searchable sequence/structure database and detailed comparative information for selected RNA structures. Sections under development are ‘RNA structure analysis’ and ‘rRNA structure-based phylogeny’.
Sequences and topology Genomes Guide: Homo Sapiens (NCBI) http://www.ncbi.nlm.nih.gov/genome/guide/ This site, within the enormous cluster of resources at the National Centre for Biotechnology Information (NCBI), provides concise information on the status of the public human genome sequencing effort. It features an intuitive interface that allows the reader to ‘tour’ the various chromosomes and view the progress in specific regions. Diseases known to be related to genes located within each chromosome are highlighted and, as would be expected, sequenced regions are available for download and analysis. Pedestrian Guide To Analysing Sequence Databases http://www.embl-heidelberg.de/~schneide/paper/springer96/ springer.html This guide, written by Burkhard Rost and Reinhard Schneider, provides an informative and practical introduction to many of the important issues concerning genomic sequence analysis. Considerable attention is paid to the prediction of protein structure from sequence information, as well as avoidance of many of the common pitfalls of computational analysis. Sacch3D: Structural Information For Yeast Proteins http://genome-www.stanford.edu/Sacch3D/ This section of the Saccharomyces Genome Database (SGD) aims to provide structural information for all proteins in the yeast genome. All experimentally solved yeast proteins are listed. Additionally, an array of computational tools has been used to predict structures for yeast proteins not yet solved.
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Protein Loop Classification http://www.bmm.icnet.uk/loop/ This resource seeks to classify different protein loop structures into particular groups according to a set of objective criteria. Each loop type can be observed using a JAVA viewer and a consensus sequence has been generated in each case. (This work has been described in a paper by B Oliva et al.: J Mol Biol 1997, 266:814-830.) Atlas of Protein Sidechain Interactions http://www.biochem.ucl.ac.uk/bsm/sidechains/index.html This site provides a detailed account of the packing arrangements formed between all possible pairings of two amino acid sidechains. Sidechain interactions are organised into positional clusters, which can be viewed in three dimensions using RasMol or Chime. The information is based on the Atlas of Protein Sidechain Interactions (J Singh, JM Thornton: Atlas of Protein Sidechain Interactions, vols I and II. Oxford: IRL Press; 1992).
HOMSTRAD http://www-cryst.bioc.cam.ac.uk/~homstrad/ The Homologous Structure Alignment Database (HOMSTRAD) consists of groups of homologous proteins that have been structurally aligned. The resultant sequence alignments are presented in the informative JOY format, which superimposes structural features upon the sequence information. Superimposed coordinates can be viewed using a Chime or RasMol viewer, and sequences can be searched against the database for homologues of known structure. GeneQuiz Homepage http://jura.ebi.ac.uk:8765/ext-genequiz/ GeneQuiz is an integrated system for automated genome analysis that uses a variety of different approaches. The homepage provides an introduction to the GeneQuiz system and some sample genome annotations were completed using this method. A link is provided to GQserve, which is a web-available version of GeneQuiz to which unknown sequences can be submitted for annotation.
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Nucleic acids Sequences and topology Web alert Judith Murray-Rust*, Jeremy H Lakey† and Eric D Scheeff‡ A selection of World Wide Web sites relevant to reviews published in this issue of Current Opinion in Structural Biology. Addresses *Crystallography Department, Birkbeck College, London WC1E 7HX, UK; e-mail: [email protected] † Laboratoire de Chimie Physique des Polymeres et Membranes, Ecole Polytechnique Federale de Lausanne, Switzerland; e-mail: [email protected] ‡ San Diego Supercomputing Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA; e-mail: [email protected] Current Opinion in Structural Biology 2000, 10:273–274
Nucleic acids Access Excellence Graphics Gallery http://www.accessexcellence.org/AB/GG/ The Access Excellence site, run by the National Health Museum, USA, offers a range of resources aimed at teachers in the biomedical area. The graphics gallery highlighted here not only has some excellent images of nucleic acid biochemistry, but also contains graphics that describe cell division, metabolism, viruses and so on. The nucleic acids section describes the Herschey–Chase experiment, the central dogma of molecular biology and models of DNA replication, to name but a few. Molecular Expressions Photo Gallery: The DNA Collection http://micro.magnet.fsu.edu/micro/gallery/dna/dna.html This is one of the pages from the Photo Gallery of the Molecular Expressions web site, which features many pages describing the world of optics and microscopy. Here, the use of polarised light microscopy enables pictures of the crystalline structure of DNA to be colourfully demonstrated. This makes a change from the over-used double helix! The New PovChem Homepage http://www.chemicalgraphics.com/PovChem/ This is the homepage of PovChem, a program that turns Protein Data Bank (PDB) files into input suitable for ray tracing with the POV-Ray program to produce high-quality images at any resolution. The results for DNA are presented here and a download facility for the software is available. The NDB Atlas of Nucleic Acid Structures http://ndbserver.rutgers.edu/NDB/NDBATLAS/index.html The Biological Structure Resource for the Nucleic Acid Database is maintained at Rutgers University, USA, with mirror sites worldwide. Among its several services, the database provides this compendium of the available nucleic acid structures, including protein–DNA and protein–RNA complexes, with full crystallographic descriptions.
Molecular Dynamics Simulations of the Glucocorticoid Receptor http://www.msi.umn.edu/Projects/mg90601/jbmsd1.html The full title is “Molecular dynamics simulations in solvent of the glucocorticoid receptor protein in complex with a glucocorticoid response element DNA sequence”. This is a web version of a paper previously published in the Journal of Biomolecular Structure and Dynamics by Harris et al. from the Abbott Northwestern Hospital Cancer Research Laboratory, Minneapolis. The figures contain JPEG movies of the dynamics of the nucleic acid and protein computed in solvent. The Comparative RNA Web Site http://www.rna.icmb.utexas.edu/ Robin R Gutell’s group at the University of Texas at Austin (Institute for Cellular and Molecular Biology) has recently established this RNA site, which includes a discussion on methods of structure prediction and methods of comparative sequence analysis, a searchable sequence/structure database and detailed comparative information for selected RNA structures. Sections under development are ‘RNA structure analysis’ and ‘rRNA structure-based phylogeny’.
Sequences and topology Genomes Guide: Homo Sapiens (NCBI) http://www.ncbi.nlm.nih.gov/genome/guide/ This site, within the enormous cluster of resources at the National Centre for Biotechnology Information (NCBI), provides concise information on the status of the public human genome sequencing effort. It features an intuitive interface that allows the reader to ‘tour’ the various chromosomes and view the progress in specific regions. Diseases known to be related to genes located within each chromosome are highlighted and, as would be expected, sequenced regions are available for download and analysis. Pedestrian Guide To Analysing Sequence Databases http://www.embl-heidelberg.de/~schneide/paper/springer96/ springer.html This guide, written by Burkhard Rost and Reinhard Schneider, provides an informative and practical introduction to many of the important issues concerning genomic sequence analysis. Considerable attention is paid to the prediction of protein structure from sequence information, as well as avoidance of many of the common pitfalls of computational analysis. Sacch3D: Structural Information For Yeast Proteins http://genome-www.stanford.edu/Sacch3D/ This section of the Saccharomyces Genome Database (SGD) aims to provide structural information for all proteins in the yeast genome. All experimentally solved yeast proteins are listed. Additionally, an array of computational tools has been used to predict structures for yeast proteins not yet solved.
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Protein Loop Classification http://www.bmm.icnet.uk/loop/ This resource seeks to classify different protein loop structures into particular groups according to a set of objective criteria. Each loop type can be observed using a JAVA viewer and a consensus sequence has been generated in each case. (This work has been described in a paper by B Oliva et al.: J Mol Biol 1997, 266:814-830.) Atlas of Protein Sidechain Interactions http://www.biochem.ucl.ac.uk/bsm/sidechains/index.html This site provides a detailed account of the packing arrangements formed between all possible pairings of two amino acid sidechains. Sidechain interactions are organised into positional clusters, which can be viewed in three dimensions using RasMol or Chime. The information is based on the Atlas of Protein Sidechain Interactions (J Singh, JM Thornton: Atlas of Protein Sidechain Interactions, vols I and II. Oxford: IRL Press; 1992).
HOMSTRAD http://www-cryst.bioc.cam.ac.uk/~homstrad/ The Homologous Structure Alignment Database (HOMSTRAD) consists of groups of homologous proteins that have been structurally aligned. The resultant sequence alignments are presented in the informative JOY format, which superimposes structural features upon the sequence information. Superimposed coordinates can be viewed using a Chime or RasMol viewer, and sequences can be searched against the database for homologues of known structure. GeneQuiz Homepage http://jura.ebi.ac.uk:8765/ext-genequiz/ GeneQuiz is an integrated system for automated genome analysis that uses a variety of different approaches. The homepage provides an introduction to the GeneQuiz system and some sample genome annotations were completed using this method. A link is provided to GQserve, which is a web-available version of GeneQuiz to which unknown sequences can be submitted for annotation.