7D dissident maps by Ernst Dieterich and Lars Lindberg

By Ernst Dieterich and Lars Lindberg

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J. Am. Chem. Soc. 127, 13,778–13,779 (2005) 48. : Accelerating conformational transitions in biomolecular systems 2, 221–232 (2006) 49. : Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J. Chem. Phys. 120(24), 11,919–11,929 (2004) 50. : Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. J. Chem. Phys. 127, 155,102 (2007) Introduction to Molecular Dynamics: Theory and Applications in Biomolecular... 27 51. : Comparative simulations of aquaporin family: AQP1, AQPZ, AQP0 and GlpF.

In principle, the chemistry-based representation should reproduce the structure and dynamics of a biomolecular system without requiring input from experimental structural data. In practice, making contact with experimental observables poses harsh challenges for these force fields both due to the level of accuracy required and the long time scales needed [54, 66]. In order to integrate experimental data in a consistent manner, biomolecular models with robust potential energy functions able to access long time scales are necessary.

Free energy via molecular simulation: Applications to chemical and biological systems. Annu. Rev. Biophys. Biophys. Chem. 18, 431–492 (1989) 14. : Scalable algorithms for molecular dynamics simulations on commodity clusters. In: Proceedings of the ACM/IEEE SC06 Conference. ACM (2006) 15. : CHARMM: The biomolecular simulation program. J. Comp. Chem. 30, 1545–1615 (2009) 16. : Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics. Wiley, New York (1989) 17. : Protein flexibility and drug design: how to hit a moving target.

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