Volume 5 Supplement 1

8th German Conference on Chemoinformatics: 26 CIC-Workshop

Open Access

Molecular simulations of peptides and proteins with Molecular Fragment Dynamics (MFD)

  • Andreas Truszkowski1,
  • Annamaria Fiethen2,
  • Hubert Kuhn2,
  • Achim Zielesny3 and
  • Matthias Epple1
Journal of Cheminformatics20135(Suppl 1):P4

DOI: 10.1186/1758-2946-5-S1-P4

Published: 22 March 2013

Molecular Fragment Dynamics (MFD) is a mesoscopic simulation technique based on dissipative particle dynamics. The method has been shown to successfully describe the phase behaviour and interfacial tensions of large chemical systems in good agreement with experimental results [1]. Unlike molecular mechanics a MFD simulation is based on "coarse-grained" molecular fragments rather than "fine-grained" atom types.

The current MFD fragment definition is based on a SMILES like one-dimensional line notation which is visualized with the Structure Diagram Generator of the Chemistry Development Kit (CDK) [2]. For an extension of the MFD technique to chemical ensembles containing peptides and proteins an appropriate molecular fragment cheminformatics tool for their design is in need.

This work provides an editor for the construction of peptides and proteins from molecular fragments. It includes building blocks for all 20 proteinogenic amino acids, their charged species and disulfide bonds. A flexible input of one-letter and three-letter amino acid codes is supported. Additionally, the editor has the capability to set charges of side chains manually or automatically.

Authors’ Affiliations

Inorganic Chemistry and Center for Nanointegration, University of Duisburg-Essen
CAM-D Technologies
Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences


  1. Schulz SG: The Phase Behavior of Amphiphilic Surfactants and Polymers: A Dissipative Particles Dynamics Study. 2004, Dissertation, Essen, University of Duisburg-EssenGoogle Scholar
  2. Steinbeck C, Han Y, Kuhn S, Horlacher O, Luttmann E, Willighagen E: The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics. J Chem Inf Comput Sci. 2003, 43: 493-500. 10.1021/ci025584y.View ArticleGoogle Scholar


© Truszkowski et al.; licensee BioMed Central Ltd. 2013

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.