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
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 Another important European collection of databases and
links is maintained at
o Christopher M. Smith of the
o G. P. Moss of Queen Mary and
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.
2. Protein Structure
o Use this link for a direct connection to the protein database that is now being maintained at
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 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
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 Juergen Suehnel at the Institute for Molecular Biotechnology
o An on-line tutorial on the Principles of Protein
Structure is available at the
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
o ProDom maintained by Jerome Gouzy
o The Center for Opiod Research and Design at the
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 Students of Professor David Macey
o Information on protein side chains can be found at the
Protein Sidechain Webpage maintained by Roland Dunbrack at the
o The Theoretical Biophysics Group at the Beckman
Institute at the
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 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 Minimotif Miner, a product of the
o The group of Professor Reshetnyak
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
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.
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
o The Japan Biological Information Research Center (SBIRC) maintains a massive database of human complementary DNA's.
o Steven Zimmerly at the
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 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 The ExPASy site in
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
o The Protein
Information Resource, maintained at
o BRENDA, a comprehensive enzyme information system, contains information on the source of the enzyme, its activities, inhibitors, substrates, products, etc.
which is maintained in
o Professor King at the
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
o Masato Nakai at the
o Refer to Christian Frosch's
Web site at the
o EMP is another enzymology database maintained at Argonne National Laboratory. The database provides provides access to thousands of references to the biochemical literature.
, 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
o The Amino
Acid Depository maintained at
o The Malaria
Parasite Metabolic Pathways site maintained at
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
o Joyce Diwan of RPI has developed Biochemistry of Metabolism, an online text to metabolism that is well illustrated by structures of enzymes.
o The Human
Protein Atlas maintained in
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.
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
o Ross Hardison and Webb
o Results of modeling on the G-protein-coupled receptors (GPCR) are available at an NIH site.
o The Peroxisome Web
Protein Kinase Resource is a database of structure and sequence information
maintained by the
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
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 David Nelson at the
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.
last updated, 7 April 2011