Bioinformatics Links Directory : Domains and Motifs

This section includes links to tools which can give information about protein domains and/or predict motifs, domains, and patterns in peptide sequences.

PRODOC - (Found July 8, 2008 )

PRODOC is a repository of domain assignments from Pfam for proteins encoded in different complete genomes and a tool for querying this information.
http://hodgkin.mbu.iisc.ernet.in/~prodoc/

PRED-GPCR - (Found July 8, 2008 )

PRED-GPCR is a tool which queries user-supplied sequences against a database of HMMs corresponding to G-protein coupled receptor (GPCR) families in order to determine which GPCR family the query sequence most resembles.
http://athina.biol.uoa.gr/bioinformatics/PRED-GPCR/

Pfam - (Found July 8, 2008 )

Collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
http://www.sanger.ac.uk/Software/Pfam/

Phospho.ELM - (Found July 8, 2008 )

Database of experimentally verified phosphorylation sites in eukaryotic proteins. Annotations are done manually and database entries come from and are linked back to scientific literature. Phospho.ELM incorporates the data formerly found in PhosphoBase.
http://phospho.elm.eu.org/

PINTS - (Found July 8, 2008 )

Patterns in Non-homologous Tertiary Structures (PINTS) finds similarities between protein structures containing structural patterns and provides a statistical measure of local structural similiarities.
http://www.russell.embl.de/pints/

PhosphoSite - (Found July 8, 2008 )

PhosphoSite is a curated database of in vivo human and mouse phosphorylation sites. The database contains peptide sequences and locations within domains and motifs for the phosphorylation sites, and links to useful resources and literature references. For educational users, information extracted from the public domain is freely available.
http://www.phosphosite.org/

PipeAlign - (Found July 8, 2008 )

PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.
http://bips.u-strasbg.fr/PipeAlign/

GraBCas - (Found July 8, 2008 )

GraBCas is a tool for predicting granzyme B and caspase cleavage sites.
http://wwwalt.med-rz.uniklinik-saarland.de/med_fak/humangenetik/software/index.html

Cascade PSI-Blast - (Found July 8, 2008 )

Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).
http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html

pdbFun - (Found July 8, 2008 )

pdbFun allows the user to search the PDB as a database of annotated residues. One can limit the search by annotations such as domains, binding sites, active sites, solvent exposure and residue type.
http://pdbfun.uniroma2.it/