A molecular fragment cheminformatics roadmap for mesoscopic simulation View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-10-04

AUTHORS

Andreas Truszkowski, Mirco Daniel, Hubert Kuhn, Stefan Neumann, Christoph Steinbeck, Achim Zielesny, Matthias Epple

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. More... »

PAGES

45

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13321-014-0045-3

DOI

http://dx.doi.org/10.1186/s13321-014-0045-3

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1050326719

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25383098


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212 grid-institutes:grid.454254.6 schema:alternateName Institute for Bioinformatics and Cheminformatics, Westphalian University of Applied Sciences, Recklinghausen, Germany
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