ProtLID, a Residue-Based Pharmacophore Approach to Identify Cognate Protein Ligands in the Immunoglobulin Superfamily

Eng Hui Yap, Andras Fiser

Research output: Contribution to journalArticle

4 Scopus citations


Members of the extracellular immunoglobulin superfamily (IgSF) play a key role in immune regulation through the control of the co-stimulatory pathway, and have emerged as potent drug targets in cancers, infectious diseases, and autoimmunity. Despite the difficult experimental access to this class of proteins, single structures of ectodomains of IgSF proteins are solved with regularity. However, the most biologically critical challenge for this class of proteins is the identification of their cognate ligands that communicate intercellular signals. We describe a conceptually novel method, protein-ligand interface design (ProtLID), to identify cognate ligands from a subproteome for a given target receptor protein. ProtLID designs an optimal protein interface for a given receptor by running extensive molecular dynamics simulations of single-residue probes. The type and location of residue preferences establish a residue-based pharmacophore, which is subsequently used to find potential matches among candidate ligands within a subproteome.

Original languageEnglish (US)
Pages (from-to)2217-2226
Number of pages10
Issue number12
Publication statusPublished - Dec 6 2016



  • ProtLID
  • Protein ligand interface design
  • immunoglobulin superfamily
  • receptor-ligand identification

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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