Titlebook: Biomolecular Simulations; Methods and Protocol Massimiliano Bonomi,Carlo Camilloni Book 2019 Springer Science+Business Media, LLC, part of

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https://doi.org/10.1007/978-3-030-33642-4 systems with rugged free-energy landscapes. This method was then applied to the protein-folding problem in combination with molecular dynamics (MD) simulation. Owing to its simplicity and sampling efficiency, the replica-exchange method has been applied to many other biological problems and has bee

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Leonard F. Koziol,Paul Beljan,Lauren Barkerding, biochemical reactions, ligand binding, and many others. Over the last several decades, enhanced sampling methods have been developed to address the large separation in time scales between a molecular dynamics simulation (usually microseconds or shorter) and the time scales of biological proces

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https://doi.org/10.1007/978-3-642-34059-8lecular dynamics (MD) simulations. Many sampling schemes rely on adding an external bias to favor the sampling of transitions and to estimate the underlying free energy landscape. Nevertheless, sampling molecular processes described by many order parameters, or collective variables (CVs), such as co

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https://doi.org/10.1007/978-3-319-07419-1prior knowledge of the system and deals with all sources of uncertainty and errors as well as with system heterogeneity. Furthermore, metainference can be implemented using the metadynamics approach, which enables the computational study of complex biological systems requiring extensive conformation

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https://doi.org/10.1007/978-3-319-07419-1allenge for experimental methods to determine high-resolution structural models. To meet this challenge, experiments are combined with molecular simulations. The latter propose models for structural ensembles, and the experimental data can be used to steer these simulations and to select ensembles t

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https://doi.org/10.1007/978-3-319-07419-1 principles, statistical inferences, and prior structural models. Here, we provide a hands-on realistic example of integrative structure modeling of the quaternary structure of the actin, tropomyosin, and gelsolin protein assembly based on electron microscopy, solution X-ray scattering, and chemical