Identification of Protein Cryptic Sites via Conformational Dynamics Capturing and Water-Based Pocket Characterization in Molecular Dynamics Simulations.

ABSTRACT: Employing molecular dynamics (MD) simulation to study the formation of novel protein cryptic sites has attracted increasing interest in the field of drug discovery. One specific challenge in this area is finding a viable method to accurately identify and characterize cryptic site transitions from MD simulation results while minimizing the need for extensive human input. Since the formation of cryptic sites often involves significant conformational changes in the protein structure, a method capable of capturing and describing these dynamic pocket transitions with precision is essential. In this paper, we present a new procedure, Conformational Dynamics Capturing and Water-Based Characterization (CDC-WBC). This procedure dynamically identifies the cryptic site region by tracking protein conf

SUBMITTER: Qu T 

PROVIDER: S-EPMC12435771 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature