DATABASES ON MEDICINE AND MOLECULAR BIOLOGY
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Active Sequences Collection
 

ASC is a collection of active protein sequences, or protein fragments or subsequences, collected in the form of function-oriented databases.
http://crisceb.unina2.it/ASC/

Blocks WWW Server
 

Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins.
A service for biological sequence analysis at the Fred Hutchinson Cancer Research Center in Seattle, Washington, USA.
http://blocks.fhcrc.org/

Bioinorganic Motif Database
 

COME is an attempt to classify metalloproteins and some other complex proteins using the concept of bioinorganic motif.
http://www.flymine.org/come/

Homologous Structure Alignment Database"  info
 

HOMSTRAD (HOMologous STRucture Alignment Database) is a curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of representative members of each family are aligned on the basis of their 3D structures using the programs MNYFIT, STAMP and COMPARER.
http://www-cryst.bioc.cam.ac.uk/homstrad/

Homology-Derived Structures of Proteins (HSSP)"  info
 

HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.
http://swift.cmbi.ru.nl/gv/hssp/

Metalloprotein Database
 

MDB contains quantitative information on all the metal-containing sites available from structures in the PDB distribution.
http://metallo.scripps.edu/

O-GlycBase"  info
 

O-GlycBase is a database of glycoproteins with O-linked glycosylation sites.
http://www.cbs.dtu.dk/databases/OGLYCBASE/

Protein Families Database of Alignments and HMMs
 

Pfam is a collection of protein families and domains. Pfam contains multiple protein alignments and profile-HMMs of these families. Pfam is a semi-automatic protein family database, which aims to be comprehensive as well as accurate.
http://www.sanger.ac.uk/Software/Pfam/

Database of S/T/Y Phosphorylation Sites
 

The Phospho.ELM database contains experimentally verified Serine, Threonine and Tyrosine sites in eukaryotic proteins. The entries, manually annotated and based on scientific literature, provide information about the phosphorylated proteins and the exact position of known phosphorylated instances.
http://phospho.elm.eu.org/

PhosphoBase - A Database of Phosphorylation Sites"  info
 

PhosphoBase contains information about phosphorylated residues in proteins and data about peptide phosphorylation by a variety of protein kinases.
http://umber.sbs.man.ac.uk/phosphabase/

The PRINTS Fingerprint Database"  info
 

PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite.
http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/

The Prosthetic Groups and Metal Ions in Protein Active Sites Database
 

Database about prosthetic groups and metal ions in protein active sites.
http://metallo.scripps.edu/PROMISE/

PROSITE Database of Protein Families and Domains
 

PROSITE is a database of protein families and domains. It is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor.
http://us.expasy.org/prosite/

PROtein TErminUS
 

ProTeus (PROtein TErminUS) is a tool for identification of short linear signatures in protein termini.
http://www.proteus.cs.huji.ac.il/

HMM Library and Genome Assignments Server"  info
 

The SUPERFAMILY database provides structural assignments to protein sequences and a framework for analysis of the results.
http://supfam.org/