- Email: [email protected]
Carbohydrates and glycoconjugates Biophysical methods
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Carbohydrates and glycoconjugates Biophysical methods Web alert Jeremy E Lakey*, Werner G Krebs† and Judith Murray-Rust‡ A selection of World Wide Web sites relevant to reviews published in this issue of Current Opinion in Structural Biology. Addresses *School of Biochemistry and Genetics, The Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK; 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] ‡Crystallography Department, Birkbeck College, London WC1E 7HX, UK; e-mail: [email protected] Current Opinion in Structural Biology 2002, 12:565–566
Carbohydrates and glycoconjugates Consortium for Functional Glycomics http://glycomics.scripps.edu/index.html This project, funded by The National Institute of General Medical Sciences (NIGMS), has the goal of defining the paradigms by which carbohydrate-binding proteins function in cellular communication. The site contains a detailed description of the technologies used and the main groups of compounds under investigation. As well as links to the Consortium’s databases, there are links to other carbohydrate databases and glyco-related Web pages. Oxford Glycobiology Institute (OGI) http://www.bioch.ox.ac.uk/glycob/ The OGI site contains details of six research areas: animal lectins; antiviral imino sugars; glycoimmunology; glycoprotein and glycolipid biosynthesis; Oxford GlycoProteomics; and structural glycobiology. Within each of these, there is a variety of descriptive material, such as reviews, a genomics resource for animal lectins, a 2D gel database and Web links. priondata.org http://www.priondata.org/ priondata.org is a huge site with data for scientists, the media, business and public use. Access is at several levels, some of which require a subscription, but within the free area there are links to the usual array of Web resources, scientific papers and researchers. The “Introduction to BSE and CJD” for the lay reader is brief, but links to several other sites with various perspectives on these diseases. Sialic acids in cellular recognition http://www.glyco.uni-bremen.de/ On first inspection, these pages, maintained by Sørge Kelm in Bremen, look a little sparse. However, they contain useful material and links, which, in addition to the well-known Thorkild’s lectin page (see below), include an area devoted to the 3D modelling of glycans. The SWEET server uses a program for constructing 3D models of saccharides from their sequences using standard nomenclature; the SWEET database contains structural and bibliographic data, and is searchable. There are
other useful online tools, including a server to predict the main mass spectrometry fragments of oligosaccharides. Thorkild’s lectin page http://plab.ku.dk/tcbh/lectin-links.htm Thorkild is Thorkild C Bøg-Hansen of the Institute of Molecular Pathology, The Panum Institute, University of Copenhagen. His lectin page is rightly renowned as a major collection, now containing over 2000 links to lectin-related material. It is extremely comprehensive and is well worth a visit for both experts and neophytes in lectin science. Glycoforum http://www.glycoforum.gr.jp/ Glycoforum describes itself as a guide to day-by-day advancing glycoscience. In addition to recently updated links, there is much excellent background material, including GlycoWord, which takes a selection of keywords, such as glycolipid, and presents intelligible articles on them from specialists in the field.
Biophysical methods CCP4 crystallography portal Web site articles http://www.ccp4.ac.uk/newsletter40/08_oasisxe.html http://www.ccp4.ac.uk/newsletter33/murshudov.html The CCP4 site, http://www.ccp4.ac.uk, is an excellent crystallographic portal site, with an extensive collection of links to crystallography-related sites on the Web. It includes a newsletter with archived articles on high-throughput structure determination and likelihood-based phasing techniques. Introduction to maximum likelihood structure refinement http://www-structmed.cimr.cam.ac.uk/Course/Likelihood/ likelihood.html This page, part of an extensive online course in protein crystallography at Cambridge University, provides an introduction to the statistical and crystallographic foundations of maximumlikelihood-based structure determination. IUCr Commission on Small-Angle Scattering http://www.iucr.org/iucr-top/comm/csas/ The IUCr Commission on Small-Angle Scattering page provides links to selected readings (including Stephen M King’s detailed introduction to the topic), as well as information on technical meetings in the field, and on commission members and their goal of building a world-wide small-angle scattering community. Fluorescence Correlation Spectroscopy — Principles and Applications http://www.mpibpc.gwdg.de/abteilungen/081/fcs/english.html This is one of the many pages on the Web that explains biophysical techniques such as fluorescence correlation spectroscopy. This one was established by the Department of Biochemical Kinetics at the Max-Planck-Institute for Biophysical Chemistry in Göttingen, Germany.
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Automated 3D electron microscopy http://www.biochem.mpg.de/baumeister/TEM/aet.html Wolfgang Baumeister supplements his review in this issue with an online introduction to the technique of automated 3D electron microscopy. The server is located at the Max-PlanckInstitute for Biochemistry in Martinsried, Germany. National Institutes of Health guide to synchrotron facilities http://www.ncrr.nih.gov/ncrrprog/btdir/SecC.asp This site lists major synchrotron facilities in the United States and includes links to the home pages of major synchrotron research groups, such as the Albert Einstein Center for Synchrotron Biosciences. These are, in turn, good starting points for information on groups currently using synchrotron facilities for biological research, including synchrotron footprinting of nucleic acids for folding studies. RNA World Web Site http://www.imb-jena.de/RNA.html This comprehensive collection of RNA resources is located at the Institut für Molekulare Biotechnologie, in Jena, Germany. It covers such diverse areas as Web-based tools, software, sequence alignment links, books, tutorials and meetings. Atlas of Nucleic Acid Structures http://ndb-mirror-2.rutgers.edu/NDB/NDBATLAS/index.html The Atlas of Nucleic Acid Structures within the NDB
(Nucleic Acid Database) highlights special aspects of NDB structures. Entries are automatically generated from the NDB using the NDBQUERY program, and include hyperlinks to atomic coordinates and graphical representations of the structure’s biological unit and crystal packing arrangement. Structures are categorised as DNA structures, RNA structures, unusual structures, protein−DNA complexes and protein–RNA complexes. Solid-state NMR in biology http://www2.bioch.ox.ac.uk/~oubsu/www/ssnmrb/ssnmrb.html This comprehensive site links numerous research groups, conferences, journals and miscellaneous pages relating to the field of solid-state NMR in biology. It is maintained by James Mason in the Department of Biochemistry at Oxford. NMR knowledge base at spectroscopynow.com http://www.spectroscopynow.com/Spy/basehtml/SpyH/ 1,2466,5-0-0-0-0-home-0-0,00.html In spite of the unwieldy URL, the NMR knowledge base at spectroscopynow.com is an impressive, commercially maintained site sponsored by Wiley. It features news, educational pages, training, jobs, links to books, information on conferences and a site for classified advertisements. The tabs at the top of the page access areas of the site dedicated to other specific spectroscopic techniques, such as UV, IR and Raman, and specific areas of research, such as spectroscopy in proteomics.
Carbohydrates and glycoconjugates Biophysical methods Web alert Jeremy E Lakey*, Werner G Krebs† and Judith Murray-Rust‡ A selection of World Wide Web sites relevant to reviews published in this issue of Current Opinion in Structural Biology. Addresses *School of Biochemistry and Genetics, The Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK; 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] ‡Crystallography Department, Birkbeck College, London WC1E 7HX, UK; e-mail: [email protected] Current Opinion in Structural Biology 2002, 12:565–566
Carbohydrates and glycoconjugates Consortium for Functional Glycomics http://glycomics.scripps.edu/index.html This project, funded by The National Institute of General Medical Sciences (NIGMS), has the goal of defining the paradigms by which carbohydrate-binding proteins function in cellular communication. The site contains a detailed description of the technologies used and the main groups of compounds under investigation. As well as links to the Consortium’s databases, there are links to other carbohydrate databases and glyco-related Web pages. Oxford Glycobiology Institute (OGI) http://www.bioch.ox.ac.uk/glycob/ The OGI site contains details of six research areas: animal lectins; antiviral imino sugars; glycoimmunology; glycoprotein and glycolipid biosynthesis; Oxford GlycoProteomics; and structural glycobiology. Within each of these, there is a variety of descriptive material, such as reviews, a genomics resource for animal lectins, a 2D gel database and Web links. priondata.org http://www.priondata.org/ priondata.org is a huge site with data for scientists, the media, business and public use. Access is at several levels, some of which require a subscription, but within the free area there are links to the usual array of Web resources, scientific papers and researchers. The “Introduction to BSE and CJD” for the lay reader is brief, but links to several other sites with various perspectives on these diseases. Sialic acids in cellular recognition http://www.glyco.uni-bremen.de/ On first inspection, these pages, maintained by Sørge Kelm in Bremen, look a little sparse. However, they contain useful material and links, which, in addition to the well-known Thorkild’s lectin page (see below), include an area devoted to the 3D modelling of glycans. The SWEET server uses a program for constructing 3D models of saccharides from their sequences using standard nomenclature; the SWEET database contains structural and bibliographic data, and is searchable. There are
other useful online tools, including a server to predict the main mass spectrometry fragments of oligosaccharides. Thorkild’s lectin page http://plab.ku.dk/tcbh/lectin-links.htm Thorkild is Thorkild C Bøg-Hansen of the Institute of Molecular Pathology, The Panum Institute, University of Copenhagen. His lectin page is rightly renowned as a major collection, now containing over 2000 links to lectin-related material. It is extremely comprehensive and is well worth a visit for both experts and neophytes in lectin science. Glycoforum http://www.glycoforum.gr.jp/ Glycoforum describes itself as a guide to day-by-day advancing glycoscience. In addition to recently updated links, there is much excellent background material, including GlycoWord, which takes a selection of keywords, such as glycolipid, and presents intelligible articles on them from specialists in the field.
Biophysical methods CCP4 crystallography portal Web site articles http://www.ccp4.ac.uk/newsletter40/08_oasisxe.html http://www.ccp4.ac.uk/newsletter33/murshudov.html The CCP4 site, http://www.ccp4.ac.uk, is an excellent crystallographic portal site, with an extensive collection of links to crystallography-related sites on the Web. It includes a newsletter with archived articles on high-throughput structure determination and likelihood-based phasing techniques. Introduction to maximum likelihood structure refinement http://www-structmed.cimr.cam.ac.uk/Course/Likelihood/ likelihood.html This page, part of an extensive online course in protein crystallography at Cambridge University, provides an introduction to the statistical and crystallographic foundations of maximumlikelihood-based structure determination. IUCr Commission on Small-Angle Scattering http://www.iucr.org/iucr-top/comm/csas/ The IUCr Commission on Small-Angle Scattering page provides links to selected readings (including Stephen M King’s detailed introduction to the topic), as well as information on technical meetings in the field, and on commission members and their goal of building a world-wide small-angle scattering community. Fluorescence Correlation Spectroscopy — Principles and Applications http://www.mpibpc.gwdg.de/abteilungen/081/fcs/english.html This is one of the many pages on the Web that explains biophysical techniques such as fluorescence correlation spectroscopy. This one was established by the Department of Biochemical Kinetics at the Max-Planck-Institute for Biophysical Chemistry in Göttingen, Germany.
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Web alert
Automated 3D electron microscopy http://www.biochem.mpg.de/baumeister/TEM/aet.html Wolfgang Baumeister supplements his review in this issue with an online introduction to the technique of automated 3D electron microscopy. The server is located at the Max-PlanckInstitute for Biochemistry in Martinsried, Germany. National Institutes of Health guide to synchrotron facilities http://www.ncrr.nih.gov/ncrrprog/btdir/SecC.asp This site lists major synchrotron facilities in the United States and includes links to the home pages of major synchrotron research groups, such as the Albert Einstein Center for Synchrotron Biosciences. These are, in turn, good starting points for information on groups currently using synchrotron facilities for biological research, including synchrotron footprinting of nucleic acids for folding studies. RNA World Web Site http://www.imb-jena.de/RNA.html This comprehensive collection of RNA resources is located at the Institut für Molekulare Biotechnologie, in Jena, Germany. It covers such diverse areas as Web-based tools, software, sequence alignment links, books, tutorials and meetings. Atlas of Nucleic Acid Structures http://ndb-mirror-2.rutgers.edu/NDB/NDBATLAS/index.html The Atlas of Nucleic Acid Structures within the NDB
(Nucleic Acid Database) highlights special aspects of NDB structures. Entries are automatically generated from the NDB using the NDBQUERY program, and include hyperlinks to atomic coordinates and graphical representations of the structure’s biological unit and crystal packing arrangement. Structures are categorised as DNA structures, RNA structures, unusual structures, protein−DNA complexes and protein–RNA complexes. Solid-state NMR in biology http://www2.bioch.ox.ac.uk/~oubsu/www/ssnmrb/ssnmrb.html This comprehensive site links numerous research groups, conferences, journals and miscellaneous pages relating to the field of solid-state NMR in biology. It is maintained by James Mason in the Department of Biochemistry at Oxford. NMR knowledge base at spectroscopynow.com http://www.spectroscopynow.com/Spy/basehtml/SpyH/ 1,2466,5-0-0-0-0-home-0-0,00.html In spite of the unwieldy URL, the NMR knowledge base at spectroscopynow.com is an impressive, commercially maintained site sponsored by Wiley. It features news, educational pages, training, jobs, links to books, information on conferences and a site for classified advertisements. The tabs at the top of the page access areas of the site dedicated to other specific spectroscopic techniques, such as UV, IR and Raman, and specific areas of research, such as spectroscopy in proteomics.