CrypToth: Cryptic Pocket Detection through Mixed-Solvent Molecular Dynamics Simulations-Based Topological Data Analysis.

ABSTRACT: Some functional proteins undergo conformational changes to expose hidden binding sites when a binding molecule approaches their surface. Such binding sites are called cryptic sites and are important targets for drug discovery. However, it is still difficult to correctly predict cryptic sites. Therefore, we introduce an advanced method, CrypToth, for the precise identification of cryptic sites utilizing the topological data analysis such as persistent homology method. This method integrates topological data analysis and mixed-solvent molecular dynamics (MSMD) simulations. To identify hotspots corresponding to cryptic sites, we conducted MSMD simulations using six probes with different chemical properties: dimethyl ether, benzene, phenol, methyl imidazole, acetonitrile, and ethylene glycol.

SUBMITTER: Koseki J 

PROVIDER: S-EPMC12152933 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature