Converting Biomolecular Modelling Data Based on an XML Representation
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doi:10.2390/biecoll-jib-2008-95
June 19, 2008
August 25, 2008
PubMed ID 20134068
Yudong Sun and Steve McKeever
Correspondence should be addressed to:
Yudong Sun
57A Victoria Road, Oxford OX2 7QF, UK
ku.ca.xo.balmoc@nullnus.gnoduy
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.