MSDmotif project is fonded by European biosapiens network.

It is dedicated to 3D and sequence motifs research and development.

The service gives statistics and allows searching based on the small 3D motifs defined by J.Milner-White like:

Beta-turn

Alpha-beta motif

Nest

ST-staple

MSDmotif is a part of MSD and it is integrated resource of sequences and 3D structures.

It combines:
• Secondary structure patterns (HTH,EETH,...)
• Phi,Psi,Chi angles
• Hydrogen and disulfide bonds within proteins (including side chain hydrogen bonds)
• Ligand interactions
• Catalytic sites
• NCBI blast sequences search
• PROSITE patterns and profiles along with PROSITE format compliant patterns

It is possible to limit the scope of a search using restrictions based on Author, keywords, experiment, resolution, and release date from this page. This page also provides links to statistics with respect to the ligand, ligand environment, patterns and 3D motifs information.

The target of the search can be based on an uploaded PDB file.

The results can be presented as charts, Ramachadran plots, with 3D and sequence multiple alignment as well as with the hit list and statistics normalization by SCOP,CATH

MSDmotif can be used as a web service too.
It provides xml query and eFamilyService xml output.
The details about xml query see here.

Other non commercial motif services:

• Small motifs by Prof. James Milner-White Dr David P. Leader University of Glasgow
• Expasy PROSITE - sequence patterns and profiles
• Motif search service
• The PRINTS Fingerprint Database
• Motif Search by Sanger Institute as part of the GeneDB project
• TOPS motifs - secondary structure motifs