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multiSMD – A Python Toolset for Multidirectional Steered Molecular Dynamics
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DOI：10.1021/acs.jcim.5c01742.png)
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Abstract
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Molecular forces govern all biological processes from cellular mechanics to molecular recognition events. Understanding the direction-dependence of these forces is particularly critical for elucidating fundamental interactions, such as protein–protein binding, ligand dissociation, and signal mechanotransduction. While steered molecular dynamics (SMD) simulations enable the study of force-induced transitions, conventional single-direction approaches may overlook anisotropic mechanical responses inherent to biomolecular systems. Therefore, probing the mechanical stability of molecular systems with respect to a director of an external force may provide critical information. Here, we present multiSMD, a Python-based tool that automates the setup and analysis of multidirectional SMD simulations in NAMD and GROMACS. By systematically probing forces along multiple spatial vectors, multiSMD captures direction-dependent phenomena, such as changing energy barriers or structural resilience, that remain hidden in standard SMD. We demonstrate the utility of our approach through three distinct applications: (i) anisotropic unbinding in a protein–protein complex, (ii) search for ligand dissociation pathways dependent on the pulling direction, and (iii) force-induced remodeling of intrinsically disordered regions in proteins. multiSMD streamlines the exploration of nanomechanical anisotropy in biomolecules, offering a computational framework to guide experiments (e.g., atomic force microscopy – AFM or optical tweezers) and uncover mechanistic properties inaccessible to single-axis methods.
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