MolData

BIOCHEMISTRY

The following are resources in Biochemistry:

1.     General Resources

o    The Tree of Life is the principal WWW resource on organismal biology.

o    BioMedNet is an annotated database of Web resources in biochemistry, medicine, and biology. You have to register but there is no fee for the use of the service. The database is fairly comprehensive.

o    The GenomeNet Web site at the Institute for Chemical Research at Kyoto University is a comprehensive, cross-linked database which provides access to information on metabolic pathways, proteins, and genomes. It is the best gateway to the biochemical literature.

o    Pedro's Tools is a frequently-touted gateway to useful resources.

o    The National Biotechnology Information Facility housed at New Mexico State University-Las Cruces maintains an extensive annotated collection of over 7000 links to sources of biotechnology information. This site provides a link to a variety of gene and protein sequence databases.

o    RESOURCES FROM THE NIH: The National Center for Biotechnology Information is a clearinghouse for the resources of the NIH and the National Library of Medicine. Molecular modeling resources are available at the NIH. Another NIH resource is the Computational Biology at the NIH Web page which includes links to software, databases, and general references.. The NIH also maintains a Glossary of Genetic Terms with examples. Finally, Medline is now available on-line through the NIH's National Library of Medicine via the PubMed site. The PubMed site also provides access to the protein database and sequence data.

o    The European Bioinformatics Institute maintains its BioModels Database, a collection of more than 50 modelling approaches. The database is described in a short review on pages 189-190 of the 14 April 2006 issue of Science.

o    The NCSA Biology Workbench is an impressive collection of databases and analysis tools used in computational biology and molecular molecular biology.

o    Keep in touch with recent developments in medicine and related sciences by visiting the Howard Hughes Medical Institute site. The journals page provides an excellent collection of links to on-line journals. The natbio page has links to sites with information on the following topics: PCR, centrifugation, combinatorial libraries, and antibodies.

o    The Geneva University Hospital and the University of Geneva hosts the ExPASy site, an important collection of access points to sequence and structural databases as well as software.

o    Another important European collection of databases and links is maintained at Heidelberg, Germany by EMBL.

o    Christopher M. Smith of the San Diego Supercomputer Center has assembled the CMS Molecular Biology Resource, a functional listing of public-domain computational tools in molecular biology. Another offering of UCSD is M.I.A. (Molecular Information Agent), a Web server that searches biological databases to find information on a macromolecule.

o    G. P. Moss of Queen Mary and Westfield College has prepared a comprehensive Web version of all to the IUBMB (International Union of Biochemistry and Molecular Biology) standards on nomenclature and structure.

o    DSMM (Database of Simulated Molecular Motions) is an impressive annotated bibliography of links to animations and movies dealing with dynamics of macromolecules. DSMM is described by G. Finocchiaro, T. Wang, R. Hoffmann, A. Gonzalez, and R. C. Wade, Nucleic Aid Research, 31, 456-457 (2003). A link to this article is provided in DSMM. A mirror site is at the Scripps Institute.

o    The Canadian Human Metabolome Project maintains the Human Metabolome Database, an extensive compendium of biological and chemical data on nearly 2,500 metabolites.

o    The Amino Acids Guide provides a concise table of properties and information for each of the essential amino acids.

2.     Protein Structure

o    Use this link for a direct connection to the protein database that is now being maintained at Rutgers University. The site also provides information on the format of .pdb files and tools to check the validity of structures deposited in the database.

o    Three-dimensional structures of proteins obtained from X-ray crystallography and NMR spectroscopy are eventually deposited in the protein database which stores the coordinates in the .pdb format. Literature references, a picture of the protein in one orientation, and the pdb file can be downloaded with the aid of the search engine.

o    Birkbeck College runs a Web course on the Principles of Protein Structure. Several of the 1996 student projects are particularly informative. A particularly complete one is Horst Schirra's page on the Determination of Protein Structure with NMR Spectroscopy..

o    3Dinsight is an integrated relational database for the structure, function, and properties of biomolecules. This Japanese Web sight provides another search engine to 3D structures.

o    The scop (structural classification of proteins) is a protein database which organizes the proteins hierachically according to their folding and structural motifs. The proteins structures can be viewed with the aid of RasMol.

o    The Glaxo Institute for Molecular Biology in Geneva uses the Swiss-Model collection of algorithms to predict the three-dimensional structure and properties of a protein. The users submits the protein sequence and the structure is returned by Email. You can also download their viewer Swiss PdbViewer from this site.

o    The EMBL site also provides an extensive collection of modeling tools which can be used to predict the structure and properties of a protein.

o    The Richardson group at Duke has developed MolProbity, a collection of tools to analyze and evaluate a protein structure from the pdb database.

o    Juergen Suehnel at the Institute for Molecular Biotechnology in Jena, Germany maintains a site that presents the structure of proteins from a number of highly informative perspectives. The site also provides information on the principles of macromolecular structure.

o    An on-line tutorial on the Principles of Protein Structure is available at the Birnbeck College site.

o    The University of Wisconsin maintains the BioMagRes Bank, a database of protein structures determined via NMR. Chemical shift data are included in the database.

o    Janet Thorton at the University College-London maintains CATH, a protein classification system. This Web page also links to an atlas of side chain interactions and analysis tools.

o    ProtoMap maintained at Hebrew University of Jerusalem offers a hierarchical classification scheme of all known proteins based on sequence comparisons.

o    PDBsum, created by Roman Laskowski, provides a visual summary of the information in the Protein Data Bank. PDBsum includes information on actives sites of proteins.

o    Michael Hecht at Princeton provides an essay on de novo protein design on his Web page.

o    ProDom maintained by Jerome Gouzy at the University of Toulouse performs homology searches of the SWISS-PROT database.

o    The Center for Opiod Research and Design at the University of Minnesota is dedicated to the opioid receptor and opioid ligands. Structures and properties of the receptor and ligands are given.

o    Figures appearing in the journal Protein Science have been collected in the Prosci site. The collection is very extensive and informative as each image which is stored in the kinemages format is accompanied by the figure caption. Special software which can be downloaded from the site is required to read the images.

o    A massive effort involving Silicon Graphics, Glaxo-Wellcome, and other European laboratories yielded predictions of the structures of over 60,000 proteins.

o    Students of Professor David Macey at Kenyon College helped write his Online Macromolecular Museum, a well designed tutorial on protein structure and function that is integrated with the structures of the proteins. The MDL utility Chime is used in the tutorials.

o    Information on protein side chains can be found at the Protein Sidechain Webpage maintained by Roland Dunbrack at the Fox Chase Cancer Center. Information is provided on the conformation and structure of monomers that define a protein structure. You must register to use the database.

o    The Theoretical Biophysics Group at the Beckman Institute at the University of Illinois has launched the Structural Biology Software Database, a database of programs of utility in the fields of structural biology and bioinformatics.

o    EMBL maintains the Macromolecular Structure Database which is oriented to protein quaternary structure. The database includes thermodynamic and structural data.

o    The Computational Biology Group at Argonne National Laboratory is developing a suite of tools for the analysis of protein structure and function. One of these is TAR-GET, a tool designed to identify classes of proteins of biological and pharmaceutical interest.

o    Disordered protein structures is the theme of the DisEMBL database from EMBL. EMBL provides a GlobPlot, a tool for measuring the tendency to disorder.

o    Chi-Ren Shyu at the University of Missouri-Columbia has developed ProteinDBS. to use it, enter the PDB ID number for a protein or a set of coordinates. The search will yield the 50 proteins most similar to the one you provided. the graphics permit a comparison of the hits.

o    Q-SiteFinder, developed at Leeds University, is a on-line modeling program that identifies the active site on a protein from its 3D structure.

o    Minimotif Miner, a product of the University of Connecticut, searches a proteinsequence for motifs associated with known function.

o    The group of Professor Reshetnyak at the University of Rhode Island maintains PFAST (Protein Fluorescence and Structure Tool Kit). The Web site provides a discussion of fluorescence from tryptophan and software for the handling of fluorescence data.

3.     Structure and Chemistry of Nucleic Acids

o    The Genome Channel maintained by Oak Ridge National Laboratory provides direct access to sequence data from a wide range of organisms.

o    Three-dimensional structures of RNA, DNA, and protein-nucleic acid complexes are accessed in the .pdb format with the aid of the indices and the search engine at the NDB database at Rutgers.

o    Application notes on nucleic acid chemistry are available at the Bioresearch section of the Beckman corporate Web site.

o    Surf the Midland site if you need to calculate the molecular weight of an oligonucleotide. Midland specializes in mass spectrometry of oligonucleotides.

o    The Operon site provides an oligonucleotide toolkit. If you provide the sequence, the toolkit will calculate useful properties such as the molecular weight and the melting temperature. Your Web browser must be Java-enabled to use the toolkit.

o    PanVera Corporation provides an on-line tutorial on the PCR technique at its Web site.

o    The Promega Web site provides the contents of its Protocols and Applications Guide. DNA typing, PCR, and restriction enzymes are covered.

o    Michael Zuker at Washington University, St. Louis has produced a Web site devoted to RNA. In addition to links to data on RNA, Zuker will use rule-based molecular mechanics to calculate the low-energy secondary structures of an RNA whose sequence you provide and the thermodynamics of folding. The Vienna RNA Package is an alternate approach for predicting the secondary structure of RNA.

o    The Japan Biological Information Research Center (SBIRC) maintains a massive database of human complementary DNA's.

o    Steven Zimmerly at the University of Calgary maintains a database of group II introns found in bacteria and archaea.

o    The ENCODE (ENCyclopedia Of DNA Elements) project of the human genome project has a Web site that will go through several phases of develoipment.

o    Two additional structural databases for RNA are the the RNA Structure Database and the RNA World Website. For folding predictions try Michael Zuker's Mfold and the Wadsworth Center's Sfold.

o    Venkatesh Murthy at the Washington University School of Medicine has developed RNABase, a tool for analyzing RNA structures generated from NMR and XRD data for errors.

4.     Enzymology and Protein Chemistry

o    KEGG, the Kyoto Encyclopedia of Genes and Genomes maintained by the Institute for Chemical Research at Kyoto University, provides maps of all known metabolic pathways with links to its protein database, DBGET, for the enzyme at each step of a pathway.

o    Two Web sites are related to systems biology: the Systems Biology Workbench and OnLine Cellular Systems Modelling. Both site provide powerful software tools to model complex coupled systems.

o    The ExPASy site in Geneva features an electronic version the the Biochemical Pathways index of Boehringer Mannheim Corp., a detailed map of metabolic pathways and enzyme biochemistry.

o    Selected metabolic maps are maintained by the PUMA project.

o    DBGET, a comprehensive interwoven protein database is maintained by the Institute for Chemical Research at Kyoto University. DBGET is linked to the major protein databases in the world and is a very effective gateway to the literature.

o    The Protein Information Resource, maintained at Georgetown University, contains data on more than 200,000 proteins. The information includes the properties and activities of each protein.

o    BRENDA, a comprehensive enzyme information system, contains information on the source of the enzyme, its activities, inhibitors, substrates, products, etc.

o    ConSurf which is maintained in Israel is a Web site organized around the evolution of proteins.

o    ProtoNet, maintained at Hebrew University, provides tools and data to analyze protein structure and function and create family trees of proteins.

o    Professor King at the Terre Haute branch of the Indiana University School of Medicine has developed The Chemicals Within, an on-line textbook in medical biochemistry.

o    Useful application notes on the purification, isolation, and characterization of proteins is provided by the Bioresearch section of the Beckman corporate Web site.

o    For information on proteases, consult either PROLYSIS a Web site at the University of Tours.

o    Masato Nakai at the University of Osaka has produced an informative Web site on the chemistry of ferrodoxin.

o    Refer to Christian Frosch's Web site at the University of Mainz for information on protein glycosylation.

o    EMP is another enzymology database maintained at Argonne National Laboratory. The database provides provides access to thousands of references to the biochemical literature.

o    CARHYD , a comprehensive and valuable list of links to all aspects of cabohydrate metabolism and enzymology, is maintained by the Facultad de Quimica y Biologia at the Universidad de Santiago de Chile.

o    The Amino Acid Depository maintained at Jena, Germany contains information on the physical and chemical properties of amino acids.

o    The Malaria Parasite Metabolic Pathways site maintained at Hebrew University links up information on the biochemical pathways in the parasite Plasmodium.

o    A related site at BioCyc, sponsored by SRI, provides databases of metabolic pathways for humans and 13 microbes.

o    Reactome is a well illustrated on-line textbook on biochemical pathways and cellular processes.

o    The MetaCyc Database is Web resource that provides data on metabolic pathways in over 240 organisms. The Web site is hosted by the National Institute of General Medical Sciences.

o    The European Bioinformatics Institute maintains ChEBI, a database of more than 2700 small-molecule substrates. It is linked to the KEGG Ligand Database.

o    Jan Jensen at the University of Iowa has developed an on-line version of PROPKA, a program that predicts and interprets pKa values of ionizable amino acid residues in proteins.

o    Joyce Diwan of RPI has developed Biochemistry of Metabolism, an online text to metabolism that is well illustrated by structures of enzymes.

o    For information on the binding of ligands to proteins, consult Heather Carlsons' MOAD (Mother of All Databases) and Shaomeng Wang's PDBbind Database.

o    The Human Protein Atlas maintained in Sweden provides graphical information on the distribution of 700 proteins in slected human cells and tissues.

o    Millipore's Interactive Biological Pathways Tool organizes metabolic pathways along the them of disease state and genetic flaws.

o    Janet Thornton of the European Bioinformatics Institute in the United Kingdom maintains Metal MACiE, a database of metal ions in catalytic enzymes such as superoxide dismutase.  The database is linked to KEGG.  The Thornton group also maintains other databases related to protein structure and function.

o    Extensive information on the human proteome is provided by the Proteomics DB which is maintained by the Technische Universitaet Muenchen.

5.     Web Pages Dedicated to Particular Protein or Protein System

o    The Kinesin Home Page covers all aspects of the structural and function of this molecular motor protein.

o    The Integrin Page is a page dedicated to the integrin family of glycoproteins that play a role in cell adhesion and the transmission of information. The page includes a useful table that summarizes information on known combinations of subunits as well as the properties of the subunits.

o    New England BioLabs maintains REBASE, an on-line database for restriction enzymes.

o    For data on cytokines, browse the R&D Systems Website which also has links to other cytokine databases.

o    Check this UCSD site for a movie which shows how molecular modelling gives insights into the function of acetylcholinesterase. This is a Java site.

o    The Kendrick-Jones' group Cambridge University maintains the Myosin Home Page, an extensive presentation of the clases of myosin molecules and their properties. The site includes structural data.

o    Ross Hardison and Webb Miller at Penn State have developed the Globin Gene Server, a database of the ca. 1000 known human globin mutations.

o    Results of modeling on the G-protein-coupled receptors (GPCR) are available at an NIH site.

o    The Peroxisome Web Site at Johns Hopkins University contains information on peoxisomes and the proteins involved in their formation. Medical disorders tied to peroxisomes are also discussed.

o    The Protein Kinase Resource is a database of structure and sequence information maintained by the San Diego Supercomputer Center.

o    The following two corporate Web sites are dedicated to human kinases and provide information on the human kinome as published in the 6 December 2002 issue of Science: Sugen and Cell Signal(click on the Refernce tab).

o    The Phosphorylation Site Database at the University of Vermont provides access to data on phosphoruylation in bacteria.

o    The HIV Protease Database hosted by NIST provides data on structures of HIV proteases and data on inhibitors. NCI AIDS Antiviral Screen, a related site sponsored by the NIH provides data on the toxicity and effectiveness of compounds used to treat AIDS.

o    The Human Mitochondrial Protein Database, another NIST product, merges information on structure and function of a host of proteins from a wide range of other databases.

o    The University of Texas Medical Branch maintains the Structural Database of Allergenic Proteins (SDAP), a Web database of allergenic proteins.

o    David Nelson at the University of Tennessee, Memphis has crafted a Web page devoted to Cytochrome P450.

o    MEROPS hosted by the Sanger Institute is an impressive database on peptidases from more than 2000 organisms. The Web site is linked to Pub Med.

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last updated, 7 July 2014