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.

One-Block CYRCA - (Found July 8, 2008 )

One-Block CYRCA is a program for identifying blocks (local ungapped profiles of the most conserved regions of protein families and domains) in a multiple sequence alignment based on the LAMA and CYRCA block-to-block alignment methods.
http://bioinformatics.weizmann.ac.il/~milana/OneCYRCA/

NRPS-PKS - (Found July 8, 2008 )

NRPS-PKS is an tool comprising four integrated databases for the analysis of large multi-enzymatic multi-domain megasynthases. The user can submit a query sequence to search for domains or view the properties of the products.
http://www.nii.res.in/nrps-pks.html

NetOGlyc Prediction Server - (Found July 8, 2008 )

Predicts mucin type GalNAc O-glycosylation sites in mammalian proteins.
http://www.cbs.dtu.dk/services/NetOGlyc/

MyHits - (Found July 8, 2008 )

The MyHits server integrates several tools with a focus on protein annotation and the analysis of protein domains. Guest users have access to tools such as ClustalW and T-Coffee and databases like Swiss-Prot, Prosite and Interpro. Registration allows users to store their results in private databases, and is free for academic users.
http://myhits.isb-sib.ch

MULTIPRED - (Found July 8, 2008 )

MULTIPRED is a tool for mapping T-cell epitopes by prediction peptides that bind to human leukocyte antigen (HLA) class I A2, A3 and class II DR supertypes.
http://antigen.i2r.a-star.edu.sg/multipred/

DBAli - (Found July 8, 2008 )

DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. Tools associated with the database allow users to mine this protein structure space by establishing relationships between protein structures and their functions.
http://salilab.org/DBAli/

CRP - (Found July 8, 2008 )

Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.
http://fasta.bioch.virginia.edu/crp/

COGs - (Found July 8, 2008 )

Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.
http://www.ncbi.nlm.nih.gov/COG/

CHOP - (Found July 8, 2008 )

CHOP takes a protein sequence as input, and returns a list of protein sequence fragments with homology to PDB and Pfam domains and to proteins from the SWISS-PROT database.
http://www.rostlab.org/services/CHOP/

CEP - (Found July 8, 2008 )

CEP (Conformational Epitope Prediction) is a server for the prediction of probable antibody binding sites of protein antigens.
http://bioinfo.ernet.in/cep.htm