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Converting Biomolecular Modelling Data Based on an XML Representation

Sun, Yudong ; McKeever, Steve

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
Biomolecular modelling has provided computational simulation based methods for investigating biological processes from quantum chemical to cellular levels. Modelling such microscopic processes requires atomic description of a biological system and conducts in fine timesteps. Consequently the simulations are extremely computationally demanding. To tackle this limitation, different biomolecular models have to be integrated in order to achieve high-performance simulations. The integration of diverse biomolecular models needs to convert molecular data between different data representations of different models. This data conversion is often non-trivial, requires extensive human input and is inevitably error prone. In this paper we present an automated data conversion method for biomolecular simulations between molecular dynamics and quantum mechanics/molecular mechanics models. Our approach is developed around an XML data representation called BioSimML (Biomolecular Simulation Markup Language). BioSimML provides a domain specific data representation for biomolecular modelling which can effciently support data interoperability between different biomolecular simulation models and data formats.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Sun, Yudong ; McKeever, Steve  (2008)  Converting Biomolecular Modelling Data Based on an XML Representation. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 5(2), 2008

Online-Journal: http://journal.imbio.de/index.php?paper_id=95
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2008/289



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