Abstract
BackgroundMesoscopic 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.ResultsThe 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 (denoted fSMILES) with connected molecular fragments to represent a molecular structure. The fSMILES 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.ConclusionsMesoscopic 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-014-0045-3) contains supplementary material, which is available to authorized users.
Highlights
Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units 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
This study aims at outlining a complete Molecular Fragment Cheminformatics (MFC) roadmap that frames a Molecular Fragment Dynamics (MFD) simulation kernel to tackle the problems sketched above
An MFC roadmap consists of four consecutive building blocks above the MFD kernel: An adequate fragment structure representation (1), a defined set of 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)
Summary
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. 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. Dissipative particle dynamics (DPD) in particular is a well-established mesoscopic simulation technique to study the structure, dynamics and properties of very large molecular ensembles which may represent millions of atoms. Its basic coarse-grained interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the fine-grained atom types of molecular mechanics but appropriate larger molecular shapes which may not necessarily be distinct chemical compounds at all [9,10,11]. Molecular fragment dynamics (MFD) is a particular chemical intuitive DPD variant: Its beads are chosen to be specific molecules or molecular fragments where each distinct chemical compound is represented by a specific set of fragments which are connected by harmonic springs in an appropriate manner to describe the intra-compound covalent bonding [17,18,19,20]
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