Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from Molecular Dynamics Simulations

Computational and Structural Biotechnology Journal 2026 Open access

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Authors: Mochammad Arfin Fardiansyah Nasution, Gert‐Jan Bekker, Suyong Re, Kenji Mizuguchi
DOI: 10.34133/csbj.0093
Cited by: 1
References: 118

Abstract

Highlights • Across 137 protein–ligand complexes (10 targets; 1.64-ms total simulation), 83.9% of top-ranked poses achieve a root-mean-square deviation ≤3.0 Å relative to experimental structures. • R -values linearly correlate with experimental p K d (0.40 to 0.94 across 4 targets), validating the stability–affinity relationship. • Functional group-level persistence pinpoints unstable moieties for stability-guided lead optimization, demonstrated using KRAS G12D inhibitors as a case study.

Fields of Study & Subjects

Robotic Mechanisms and Dynamics Robot Manipulation and Learning Control and Stability of Dynamical Systems

Publication details

Journal / source
Computational and Structural Biotechnology Journal
Publisher
American Association for the Advancement of Science (AAAS)
Volume
35
Issue
1
Pages
0093–0093
Publication date
1 March 2026
Language
EN