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Updated: Sep 17, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
An automated analytical framework for identifying reaction channels and structural evolution in multi-channel
Hangxu Liu1,2, Yifei Zhu1,2, Zhenggang Lan1,2
1MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, People's Republic of China.
Abstract:
The automatic identification of reaction channels and key nuclear motions from nonadiabatic dynamics simulations remains a major challenge. Traditional manual analysis is inefficient and relies heavily on expert intuition, creating a bottleneck for interpreting complex photochemical processes. To overcome this challenge, we introduce an automated analytical framework that integrates unsupervised learning (dimensionality reduction, clustering, and information entropy) with conical intersection validation to directly extract key dynamical information from on-the-fly trajectory surface hopping data. Our method effectively determines multi-channel reaction pathways and successfully identifies their key structural nuclear motions. When applied to keto-isocytosine and methaniminium cation, the framework successfully recovers all known reaction channels and their characteristic coordinates, demonstrating its reliability. This work provides an effective, objective, and reproducible approach for transforming raw trajectory data into clear mechanistic insights in excited-state dynamics.
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