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Front. Chem. | doi: 10.3389/fchem.2019.00400

CherryPicker: An Algorithm for the Automated Parameterisation of Large Biomolecules for Molecular Simulation

  • 1School of Biological Sciences, Faculty of Science, University of Auckland, New Zealand

Molecular simulations allow investigation of the structure, dynamics and thermodynamics of molecules at an atomic level of detail, and as such, are becoming increasingly important across many areas of science. As the range of applications increases, so does the variety of molecules. Simulation of a new type of molecule requires generation of parameters that result in accurate representation of the behaviour of that molecule, and, in most cases, are compatible with existing parameter sets. While many automated parameterisation methods exist, they are in general not well suited to large and conformationally dynamic molecules. We present here a method for automated assignment of parameters for large, novel biomolecules, and demonstrate its usage for peptides of varying degrees of complexity. Our method uses a graph theoretic representation to facilitate matching of the target molecule to molecular fragments for which reliable parameters are available. It requires minimal user input and creates parameter files compatible with the widely-used GROMACS simulation software.

Keywords: Molecular dynamics (82A71), Fragment matching, automated parameterisation, biomolecules, GROMOS force field, graph theory

Received: 27 Nov 2018; Accepted: 17 May 2019.

Edited by:

Thomas S. Hofer, University of Innsbruck, Austria

Reviewed by:

Arnab Mukherjee, Indian Institute of Science Education and Research, Pune, India
Sam P. De Visser, University of Manchester, United Kingdom
Krzysztof B. Bec, University of Wrocław, Poland  

Copyright: © 2019 Allison and Welsh. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Jane R. Allison, School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, Auckland, New Zealand, j.allison@auckland.ac.nz