Valuable information about membrane protien function and structure can be gained from small structure/sequence pattern. MeMotif is a database of linear motifs in alpha-helical transmembrane rpoteins, accessible trhough a wiki-based web-server. Sequential motifs are derived from hierarchical clustering of protein fragments from knwon alpha-helical transmembrane protein structures. Fragments are clustered according to common patterns of hydrogen bonds or similar backbone torsion angle profiles. Each cluster is then associated to a regular expression and functional characterization.

Each sequence motif is provided with a detailed functional description, statistics and cross-links to bioinformatics databases such as Uniprot, Prosite, GO, Pfam, SCOPPI, PDB and GoPubmed. This knowledge is made available to the scientific community through a wiki system and can be edited, corrected and enriched from experts in different fields from structural biology. The annotated motifs can be used in different biological application such as functional characterization of new sequences, modeling of transmembrane proteins and design of mutagenesis experiments.

Some examples of already annotated motifs are:

• Putative helix-helix packing motif at the end of alpha-helices A-F-[MV]-G-[FY]
• Loop motif in cytochrome b F-F-G-V-x-[AGT]-[FIM]
• Interface helix motif in subunit III of bc1 complex G-L-Y-Y-G-S-Y
• Across families membrane-water interface helix motif L-x-S-I-[GP]
• Cross-family reentrant motif L-[AT]-G-[FI]-[AILV]-x-[IPV]-[IL]
• Heme packing motif in cytochrome b L-[IMV]-x-Q-I-[LV]-T-G-[IL]
• Loop motif in cytochrome c and quinol oxidases P-[AS]-G-G-G-D-P-[IV]
• Loop motif in cytochrome b P-[DN]-x-L-G-[DH]-P-[DE]
• Across families helix-helix packing motif V-G-x-L-[ACTV]-[AGT]-[IL]-[AGV]
• Across families TrpPhe kink motif W-L-F-[ST]

You can search in the Database by the following options (for more details see Search):