A molecular fragment cheminformatics roadmap for mesoscopic simulation.
BACKGROUND
Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application.


RESULTS
The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denotedfSMILES) with connected molecular fragments to represent a molecular structure. ThefSMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software.


CONCLUSIONS
Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and conceptual usage hurdles. Molecular Fragment Cheminformatics may be regarded as a crucial accelerator to propagate MFD and similar mesoscopic simulation techniques in the molecular sciences. Graphical abstractA molecular fragment cheminformatics roadmap for mesoscopic simulation.
Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Essen, Germany.
Andreas
A
Truszkowski
Institute for Bioinformatics and Cheminformatics, Westphalian University of Applied Sciences, Recklinghausen, Germany.
Mirco
M
Daniel
CAM-D Technologies, Essen, Germany.
Hubert
H
Kuhn
GNWI - Gesellschaft fuer naturwissenschaftliche Informatik mbH, Oer-Erkenschwick, Germany.
Stefan
S
Neumann
Chemoinformatics and Metabolism, European Bioinformatics Institute (EBI), Cambridge/Hinxton, UK.
Christoph
C
Steinbeck
Institute for Bioinformatics and Cheminformatics, Westphalian University of Applied Sciences, Recklinghausen, Germany.
Achim
A
Zielesny
Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Essen, Germany.
Matthias
M
Epple
Computer simulation; Dissipative particle dynamics; Fragment smiles; Mesoscopic simulation; Molecular fragment cheminformatics; Molecular fragment dynamics; Molecular fragmentation; Peptide representation; Protein representation; fSmiles