Databases such as NRL-3D and
information about the overall three-dimensional structures of proteins.
As an analogy, if you looked up a name in the phonebook, this would be
the yearbook that would show his or her picture.
In order to find out virtually anything you want to know about an enzyme,
use the EC
Enzyme Database. This database can be searched using the name of the
enzyme. A series of different enzymes )with associated EC numbers) will
come up. When you click on a particular type of enzyme (EC number), it
will lead you into a page that contains links to other types of
information, including: the reaction catalyzed, associated metabolic
diseases (OMIM), and what
is known about enzymes from particular organisms. When you in turn click
on an enzyme from a particular organism you will be led to a page that
contains links to protein sequence,
pattern, and structure for that enzyme.
The CATH database, maintained at University College London, provides a hierarchical domain classification of protein structures in the Brookhaven protein databank. The site's glossary - like BioTech a "work in progress" - may prove helpful for those new to the language of protein classification. On the other hand, if you are new to protein classifications then CATH may be too arcane for you.
DBGET is a science links database that
summarizes the major databases for nucleic acids,
proteins, ligands, medicine, etc. It could prove
useful for those trying to cross-reference
Incorporating the information on EMBL,
GenBank, Swiss-Prot and others, Genobase is a
comprehensive molecular biology database covering
nucleic acid, proteins, structure, etc.
initial searches for protein information, Swiss Prot generates
search returns that are straightforward and very informative. The database
is organized by EMBL accession numbers but is searchable by description,
identification, author, date, and more.
PIR -- The Protein Information
A collection of other databases,
PIR compiles protein information based on what is known about each protein.
As such, this could be a very useful tool for anyone seeking data on
obscure proteins. Conversely, it could overwhelm those looking for
information on well-studied proteins with too much information.
Rather simple, this
database compiles information from some of the bigger databases such as Swiss Prot,
GenBank, and others. Unlike the more comprehensive databases, though, OWL
tends to present more concise versions of the information. This makes OWL
ideal for students who do not want massive amounts of data return or for
anyone who wants just the basic facts about the protein.
This server allows for quick comparisons between unknown sequences and those
found within the Genome Sequence Database, Swiss Prot, Prosite and PDB.
Molecular Biology Server -
Aside from the sequence
identification provided by most databases, the ExPASy site provides a
number of tools for protein analysis including peptide mass calculations,
amino acid matching between sequences, nucleic acid sequence translation
to protein, and much more. There are also tools to aid in structure projections
Based on the homologous domains from Swiss Prot, this database provides
information on the domain arrangement of proteins and consensus sequences.
This is a database that searches for sequence homology based on blocks,
"multiply aligned ungapped segments corresponding to the most highly conserved
regions of proteins." These blocks are determined by cross-referencing
several databases for highly conserved sequence regions.
Database of Proteins of Immunological Interest -
Because this is a gopher-based database, searchers should have some
idea of what they are looking for.
A protein domain sequence databse, SBASE is cross-
referenced with most of the other major sequence databases. This
database, therefore, can provide the same information as others,
but the interface is not as user-friendly.
Chemical MIME Connection -
All the molecules and chemical
structure images off the Web can be quite confusing without a
little understanding of some of the image formats and viewing
software. Marilynn Dunker's site briefly explains the different
types of computer images one might find and provides links to other
sites where software and images can be downloaded. This site could
be particularly invaluable for beginners.
SCOP - Structural Classification of Proteins -
As its name implies,
SCOP classifies all proteins for which science has structural
information in order to examine the relationships between proteins.
The result is a database with a wealth of structural information
on folding patterns, sequence, phylogeny and more.
Not only does NRL 3D provide protein
sequence and structural information, it also serves as a link
between the Protein Data Bank
and certain structural manipulation software which cannot interpret
the information from PDB. Although very informative, searching
can be a little tricky, and reading the instructions is very
Library of Biological Macromolecules -
This gopher-based site contains hundreds of images
of molecules and complexes along with the reference
information. Images are well-categorized although
entering with a specific goal would be helpful.
Protein Motions Database -
This database provides
information on the movements of proteins.
Acid Properties -
This site contains
a grotesquely large amount of information about
amino acids including structure, pKa, geometry,
solubility, images, etc..
This database was designed to provide information
on enzymes as they were discovered and characterized. Recently,
though, the server has been finicky in responding and may
not provide much if any information at all.
REBASE: The Restriction Enzyme Database -
REBASE is a comprehensive
database with everything one would want to know about
an enzyme. User-friendly, it provides references and
other resources in addition to the expected sequence, function
and structural information.
SWISS-2D: Two-Dimensional Polyacrylamide Gel Electrophoresis
Swiss-2D references proteins to
2D PAGE maps. This provides a source for comparisons of
proteins relative to others by size, shape, etc.
This center focuses on the design and analysis of protein databases.
As such, this site provides links to other similar resources. Protein
information at this site is derived from 2D PAGE gels.