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SWISS-PROT
OWL
PIR Protein Information Resource
Search Databases at EBI (EMBL)
Search Databases at NCBI (GenBank)
BLAST search of databases at NCBI
BLAST search of databases at NCGR
BLASTula, the server of Blast servers
BLAST2 search of databases at EMBL
BLITZ search of databases at EBI
SAS - Sequence Annotated by Structure
ProtoMap: An automatic hierarchical classification of all swissprot proteins
EMBL Sequence Alerting System
MIPS Sequence Alerting System
Expasy Sequence Alerting System
EC Enzyme Database
BRENDA - experimental information on enzyme function
MIPS - a database for protein sequences and complete genomes
Kabat Database of Proteins of Immunological Interest
Protein Research Foundation (PRF)
HotMolecBase
QUEST Protein Database Center
2-D PAGE Databases
NRL_3D Protein Sequence Structure Database
O-GlycBase - O-glycosylated proteins
PROLYSIS - protease and protease inhibitors
PhosphoBase - a database of phosphorylation sites
Amino Acid Information
PROWL - Databases, Knowledgebases, Software
SWISS-PROT
SwissProt is a curated protein sequence database which strives to provide a
high level of annotations (such as the description of the function of a
protein, its domains structure, post-translational modifications, variants,
etc), a minimal level of redundancy and high level of integration with other
databases.
SWISS-PROT was established in 1986 and is maintained collaboratively, since 1987, by the Department of Medical Biochemistry of the University of Geneva and the EMBL Outstation - The European Bioinformatics Institute (EBI).
OWL
OWL is a non-redundant composite protein sequence database
produced from the following source databases
SWISSPROT, PIR 1-3, GenBank (translations), Brookhaven.
PIR Protein Information Resource
PIR is an integrated protein information resource,
utilizing information from the DNA Database in Japan (DDBJ)
and the Martinsried Institute for Protein Sequences (MIPS).
Search Databases at EBI (EMBL)
The EBI provides facilities to search for sequences by text or by
sequence similarity and to submit new sequences.
Search Databases at NCBI (GenBank)
The NCBI provides facilities to search for sequences by text or by sequence simi
larity
and to submit new sequences.
BLAST search of databases at NCBI
BLAST is a program that allows you to search for similarity between your query
sequence and the gene sequences held at the NCBI.
BLAST search of databases at NCGR
BLAST is a program that allows you to search for similarity between your query
sequence and the gene sequences held at the NCGR.
BLASTula, the server of Blast servers
BLASTula, the server of Blast servers: a group of pages offering a unique
access to more than 40 different Blast servers world-wide operating on
original sets of sequences.
BLAST2 search of databases at EMBL
BLAST2 is a program that allows you to search for similarity between your query
sequence and the gene sequences held at EMBL. It is similar to the original BLAS
T program, but it includes gaps in the alignments.
BLITZ search of databases at EBI
BLITZ does a very sensitive and extremely fast comparison
of your protein sequences
against the Swiss-Prot protein sequence database using the Smith and Waterman be
st local similarity
algorithm.
SAS - Sequence Annotated by Structure
SAS is a tool which aims to bridge the gap between protein sequence and
structural analysis, and aid identification of a protein sequence, by
using structural information to recognise distant homologues.
SAS can apply key structural features to the results of sequence or threading searches at a sequence level. Residues in the sequences of known structures are coloured by selected structural properties, and are displayed using a Web browser or downloadable PostScript file.
ProtoMap: An automatic hierarchical classification of all swissprot proteins
This site offers an exhaustive classification of all the proteins in the
swissprot database, into groups of related proteins.
The resulting classification splits the protein space into well defined groups of proteins, most of them are closely correlated with natural biological families and superfamilies. The hierarchical organization may help to detect finer subfamilies that make up known families of proteins as well as interesting relations between protein families.
EMBL Sequence Alerting System
The sequence alerting system search each day in several databases for
news on (homologues of) "your" sequence and will inform you by email if
it has detected a new relative.
DNA and protein sequences are accepted as query, but only protein databases are screened. You can specify some parameters of the searches in order to optimise it for your particular problem.
MIPS Sequence Alerting System
Every day, new protein sequences are added to the protein and nucleic
acid databases. The Alert utility is designed to keep you abreast of
these changes by sending you once per week, via email, the new database
entries related to your field of interest.
You can specify a peptide sequence from 3 to 30 amino acids in length and keywords in the various annotation fields
Expasy Sequence Alerting System
New Protein Sequences, which are added to the Swiss-Prot database on a
weekly bases can be scanned following a user-defined query. The
searches are performed on the current non-cummulative weekly additions
only. This will allow researchers to be aware of new protein sequences,
related to their interests, before the actual database release.
All Results will be returned to you via E-mail.
You can specify peptide sequences, or Prosite-style patterns or keywords in the various annotation fields.
EC Enzyme Database
This is a repository of information relative to the nomenclature of
enzymes. It is primarily based on the recommendations of the
Nomenclature Committee of the International Union of Biochemistry and
Molecular Biology (IUBMB) and it describes each type of characterized
enzyme for which an EC (Enzyme Commission) number has been provided.
BRENDA - experimental information on enzyme function
This experimental data has been carefully collected and checked over
many years at the German National Biotechnology Lab in Braunschweig in a
project led by Dietmar Schomburg, now of Cologne university. The
biochemists involved in the project included, among others, Dr. Doerte
Stephan, Margit Salzmann, Dr. Ida Schomburg, and Cornelia Munaretto.
The data is also published in The Enzyme Handbook (Springer).
MIPS - a database for protein sequences and complete genomes
This gives quick access to the results of analysing the protein in various genomes:
Kabat Database of Proteins of Immunological Interest
This includes amino
acid sequences, related nucleotide sequences and aligned
sequences. It is maintained by Dr. C. Wu, Technological
Institute, Northwestern University.
Protein Research Foundation (PRF)
Comprehensive bibliographies of:
HotMolecBase
HotMolecBase is a collection of biomedically interesting molecules like
p53, prion protein, huntingtin, presenilin-1, and others. The entries
for those molecules cover details about their cellular and molecular
biology that cannot be found somewhere else on the web in this
concentrated form. Their involvement in diseases, together with medical
applications (progress in diagnosis and treatment), is also included.
HotMolecBase focusses on especially promising molecules that are
potential targets for drug development.
QUEST Protein Database Center
Data generated by two-dimensional (2D) electrophoresis of proteins on
polyacrylamide gels are available from CSHL.
2-D PAGE Databases
The Danish Centre for Human Genome Research's 2-D PAGE
Databases contain data on proteins
identified on various 2-D PAGE reference maps.
NRL_3D Protein Sequence Structure Database
This is a protein sequence database derived from high
resolution x-ray structures of proteins deposited in the
Brookhaven National Laboratory's Protein Data Bank (PDB). It
is distributed by the Protein Information Resource (PIR), at
the National Biomedical Research Foundataion.
O-GlycBase - O-glycosylated proteins
O-GLYCBASE is a revised database of O-glycosylated proteins. Version
2.0 has 127 glycoprotein entries containing 627 O-glycosylation sites.
The criteria for inclusion are at least one experimentally verified
O-glycosylation site. The terminal sugar linked to serine or threonine
is cited when known. The database is non-redundant in the sense that it
contains no identical sequences. Mucins have tandem repeat sequences,
which are O-glycosylated. This results in some redundancy of the
O-glycosylation sites.
PROLYSIS - protease and protease inhibitors
This is a resource for those interested in
proteases and their natural or synthetic inhibitors.
PhosphoBase - a database of phosphorylation sites
PhosphoBase is a revised database of phosphorylation sites in proteins. Information about the position
of phosphorylated serines, threonines, or tyrosines and relevant kinetic parameters are presented.
PROWL - Databases, Knowledgebases, Software
Databases
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