Cellular and Molecular Bioengineering

, Volume 2, Issue 3, pp 366–374

Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics


DOI: 10.1007/s12195-009-0084-4

Cite this article as:
Parker, D., Bryant, Z. & Delp, S.L. Cel. Mol. Bioeng. (2009) 2: 366. doi:10.1007/s12195-009-0084-4


Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed by combining groups of atoms into a system of rigid bodies connected by joints. Contacts between rigid bodies enforce excluded volume constraints, and spring potentials model system elasticity. This simplified representation allows the conformations of complex molecular motors to be simulated interactively, providing a tool for hypothesis building and quantitative comparisons between models and experiments. In an example calculation, we have used the software to construct atomically detailed models of the myosin V molecular motor bound to its actin track. The software is available at www.simtk.org.


Molecular simulation Myosin V Protein kinematics Open-source software 

Supplementary material

12195_2009_84_MOESM1_ESM.doc (58 kb)
Supplementary material 1 (DOC 59 kb)

Copyright information

© Biomedical Engineering Society 2009

Authors and Affiliations

  1. 1.Department of Mechanical EngineeringStanford UniversityStanfordUSA
  2. 2.Department of BioengineeringStanford UniversityStanfordUSA
  3. 3.Schools of Medicine and Engineering Clark Center, Stanford UniversityStanfordUSA

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