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Dr. Lim, Carmay

Emeritus Research Fellow
  • +886-2-2789-9043 (Lab) (Room No: N117)
  • +886-2-2652-3031 (Office)
  • +886-2-2788-7641 (Fax)

  • Computational Biophysics
  • Computational Chemistry
  • Bioinformatics

Education and Positions:
  • 1984, Ph.D. in Chemical Physics, University of Minnesota, Minneapolis

    1979, B.S. in Chemistry, Royal Holloway College, London University


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PPI-Hotspot DB: Database of Protein-Protein Interaction Hot Spots

Dr. Lim, Carmay
Journal of Chemical Information and Modeling, Feb 11, 2022

Single-point mutations of certain residues (so-called hot spots) impair/disrupt protein-protein interactions (PPIs), leading to pathogenesis and drug resistance. Conventionally, a PPI-hot spot is identified when its replacement decreased the binding free energy significantly, generally by ≥2 kcal/mol. The relatively few mutations with such a significant binding free energy drop limited the number of distinct PPI-hot spots. By defining PPI-hot spots based on mutations that have been manually curated in UniProtKB to significantly impair/disrupt PPIs in addition to binding free energy changes, we have greatly expanded the number of distinct PPI-hot spots by an order of magnitude. These experimentally determined PPI-hot spots along with available structures have been collected in a database called PPI-HotspotDB. We have applied the PPI-HotspotDB to create a nonredundant benchmark, PPI-Hotspot+PDBBM, for assessing methods to predict PPI-hot spots using the free structure as input. PPI-HotspotDB will benefit the design of mutagenesis experiments and development of PPI-hot spot prediction methods. The database and benchmark are freely available at https://ppihotspot.limlab.dnsalias.org.