Development of a program for complex-ligand system setup in molecular dynamics simulations with binding pose metadynamics integration

Martín López, Eva

Development of a program for complex-ligand system setup in molecular dynamics simulations with binding pose metadynamics integration

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Martín López, E. Development of a program for complex-ligand system setup in molecular dynamics simulations with binding pose metadynamics integration. 2023. handle: http://hdl.handle.net/10230/59918

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Abstract

In this study we introduce a new Python package that automates the preparation of proteinligand systems for Molecular Dynamics (MD) simulations, ensuring reproducibility of results by minimizing the need of manual intervention. Our package integrates popular open-source MD libraries, featuring user-friendly tutorials that ensure accessibility for researchers with varying levels of expertise. Additionally, the program incorporates Binding Pose Metadynamics (BPMD), a technique that enables the identification of stable ligand poses. We demonstrate the program's effectiveness through benchmark metadynamics simulations, demonstrating its accuracy in MD system preparation and exploration of different proteinligand binding poses. Our tool features a detailed workflow, providing a straightforward approach to prepare protein-ligand complexes from non-curated PDB structures.