What are Linear Motifs (LMs) ?

About 15-40% of all protein-protein interactions (PPIs) in the cell are estimated to be mediated by very short peptide segments that approximately conform to specific sequence patterns known as linear motifs. These mainly participate in signaling and regulatory networks, and are implicated in many disease processes like cancer and neurodegerative disorders.

About LMPID:

LMPID (Linear Motif mediated Protein-Protein Interaction Database) is a manually curated database which provides comprehensive experimentally validated information about the LMs mediating PPIs from all organisms on a single platform.

LMPID provides two options to its users: (a) Search  and  (b) Browse

The Search option on the homepage allows users to query the database with specific keywords for the Motif Instance, Regular Expression, UniProt Accession, UniProt Identifier & Gene Name of the protein containing the motif, Name of the domain interacting with the motif and Diseases associated with the motif instance:

The result page provides information on the motif regular expression, sequence, position in the protein, interacting domain and links to

• the UniProt page of the protein containing the motif,

• the PubMed page of the referenced research articles that report the experimental studies for the motif,

• a page of the database describing the two proteins interacting with each other through the motif

  

  Clicking on the 'Interaction ID' opens the following page:
  

  

To use the Browse option, click on the 'Browse' tab:

The Browse page lists all instances in the database-

1. In alphabetical order of the Gene names of Bait proteins containing the LMs.
   

   

2. According to the Domain interacting with the LM.
   

   

        Sample Output:

The following abbreviations have been used for denoting the experimental procedures:

•     AP-MS : Affinity purification-mass spectrometry


•     BiFC : Bimolecular fluorescence complementation assay


•     BLI : Bio-Layer Interferometry


•     CD : Circular dichroism spectroscopy


•     ChIP : Chromatin Immunoprecipitation


•     Co-IP : Co-immunoprecipitation


•     ELISA : Enzyme-linked immunosorbent assay


•     FRET : Fluorescence resonance energy transfer


•     GPC : Gel permeation chromatography


•     GST : Glutathione S-transferase


•     His : Histidine


•     ITC : Isothermal titration calorimetry


•     NMR : Nuclear magnetic resonance spectroscopy


•     PAX-MS : Peptide array X-linking-mass spectrometry


•     SPR : Surface plasmon resonance


•     Y2H : Yeast two-hybrid assay

If you are using this database please cite:
Sarkar, D., Jana, T., & Saha, S. LMPID: a manually curated database of linear motifs mediating protein-protein interactions. Database (2015) Vol. 2015: article ID bav014; doi:10.1093/database/bav014   PMID:25776024