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
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
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
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 The
o Juergen Suehnel at the Institute for Molecular Biotechnology
in
o An on-line tutorial on the Principles of Protein
Structure is available at the
o 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
at the
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 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
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 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
o Minimotif Miner, a product of the
o The group of Professor Reshetnyak
at the
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 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
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
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.
o ConSurf
which is maintained in
o ProtoNet,
maintained at
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.
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
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 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
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
Miller at
o Results of modeling on the G-protein-coupled receptors
(GPCR) are available at an NIH
site.
o The Peroxisome Web
Site at
o The
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 The
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