Extending the horizon: towards the efficient modeling of large biomolecular complexes in atomic detail
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- Feig, M., Chocholoušová, J. & Tanizaki, S. Theor Chem Acc (2006) 116: 194. doi:10.1007/s00214-005-0062-4
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The application of evaluation of implicit solvent methods for the simulation of biomolecules is described. Detailed comparisons with explicit solvent are described for the modeling of peptide and proteins in continuum aqueous solvent. In addition, we are presenting new data on the simulation of DNA with implicit solvent and describe the development of a heterogeneous dielectric model for the simulation of integral membranes. The performance of implicit solvent simulations based on the GBMV generalized Born method is compared with explicit solvent simulations, and implications for the simulation of very large biomolecular complexes is discussed. We are anticipating that the work described herein will lead to new, efficient modeling tools that will allow the simulation of longer timescales and larger system sizes in order to meet current and future challenges by the experimental community.