1. Content of the Database
The NMP-db
consists of two parts. The first part is the actual
literature based NMP-db, containing all nuclear matrix
proteins (NMPs) that were originally found in PubMed.
The second part is a database of homologues to the
NMP-db proteins. This database is called NMP-db(hom)
and contains proteins which have at least an HSSP-value
of 55 to one of the proteins in the NMP-db.
The NMP-db holds informations about the protein names,
their organism and the cell-type in which NM
association was observed. Also links to the respective
PubMed abstracts are given in each entry.
Additionally, we provide information about predictions
of secondary structure, solvent accessibility,
coiled-coil regions and domain-architecture, as well as
the sequence, links to PDB (database of 3D-structures),
molecular weight, theoretical pI, links to
SWISS-2DPAGE, OMIM, PEP and many other databases.
If available, we also list regions in a protein
sequence that are known to be cruicial for
NM-targeting.
Finally, links to the S/MARt DB allow users to find
DNA-regions that bind to NMPdb proteins.
2. Structure and Fields of the Database
The
following fields can be accessed in the database:
3. How to browse NMPdb
You can browse
through the NMPdb instead of searching for a specific
protein by going to the browse page and look for a
feature (organism, molecular weight, etc.) that you
would like specify. Simply click on a link and you will
get to a page that lists all database entries in a
sorted fashion matching the criteria you picked.
4. How to use the Advanced-Search
The
advanced search lets you specify up to three search
terms, for which you want to look in different fields
of the database. If you need less terms, leave the
remaining query-fields empty. The search-terms can be
connected by the following operators:
AND: the term that follows this operator has
to occur in the specified field(s)
OR: either the preceding or the following term
to this operator has to appear in the specified
field(s)
AND NOT: the search-term following this
operator must not show up in the specified
field(s)
For each search field you can additionally set
whether you want it to be case sensitive.
Lastly pick a database that you want to search in:
NMP-db, NMP-db(hom) or both.
For example: if you want to search for all proteins
that bind to DNA in human, you could try the following
search query:
Keywords: DNA-binding AND Organism: human
(case-insensitive)
5. Download the Database
Go to the
download-page and pick a database
and a compression type (zip or tar.gz). Then download
the files and uncompress them on your machine. The
databases are simple ASCII-files.
5. Citation
If you use the NMP-db, please
cite the following paper in your publication:
Mika S., Rost B.
NMPdb: database of Nuclear-Matrix Proteins
Nucleic Acids Research (submitted)