Helix Positioner

Helix Positioner (HPer) is a computational tool to identify potential binding sites for single helical peptides at protein-protein interfaces. The tool aims to expand the possibilities for designing peptide modulators of protein-protein interactions (PPIs) beyond the native binding helices or sites.

Key features of HPer:

1. Locates single-helix binding sites at protein-protein interfaces based on the structure of the target proteins.

2. Performs well on known single-helix-mediated PPIs, recapturing key interactions and hot-spot residues of native helical binders.

3. Screens non-helical-mediated PPIs in the PDBbind database to identify PPIs suitable for helical peptide binding and predict the helical binding sites for designing novel peptide ligands.

4. Provides a protocol for designing novel helical peptide ligands on the identified binding sites, as demonstrated with the L2 domain of EGFR.

5. Allows further investigation of the binding stability of designed sequences using molecular dynamics simulations.

Topic

Small molecules;Protein interactions;Protein binding sites;Immunoproteins and antigens;Protein folding, stability and design

Detail

  • Operation: Molecular dynamics;Protein interaction prediction;Protein-protein binding site prediction

  • Software interface: Command-line interface

  • Language: C

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: The National Natural Science Foundation of China, Ministry of Science and Technology of the People's Republic of China.

  • Input: -

  • Output: -

  • Contact: Changsheng Zhang changshengzhang@pku.edu.cn ,Luhua Lai lhlai@pku.edu.cn

  • Collection: -

  • Maturity: -

Publications

  • Discovery of novel helix binding sites at protein-protein interfaces.
  • Yang W, et al. Discovery of novel helix binding sites at protein-protein interfaces. Discovery of novel helix binding sites at protein-protein interfaces. 2019; 17:1396-1403. doi: 10.1016/j.csbj.2019.11.001
  • https://doi.org/10.1016/J.CSBJ.2019.11.001
  • PMID: 31768230
  • PMC: PMC6872852

Download and documentation

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