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Protein Modelling pp 165–174Cite as

Molecular Mechanics/Coarse-Grained Models

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Abstract

Molecular simulations have proved to be extremely successful in predicting structures and energetics of ligand binding to their target receptors. However standard approaches are challenged when one has to deal with homology models based on templates with low sequence identity. In an effort at facing this challenge we have developed a hybrid molecular mechanics/coarse-grained (MM/CG) simulations approach, aimed at connecting the disparate spatial and temporal scales relevant to complex biological processes. This approach concentrates the efforts in characterizing the binding cavity while renouncing to most of protein details which are likely to be predicted in a rather inaccurate way by bioinformatics techniques. Examples of application of this technique to GPCRs illustrate the power of this approach.

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Author information

Authors and Affiliations

  1. Computational Biophysics, German Research School for Simulation Sciences, Jülich, Germany

    Alejandro Giorgetti

  2. Department of Biotechnology, University of Verona, Ca’ Vignal 1, Verona, Italy

    Alejandro Giorgetti

  3. Computational Biophysics, German Research School for Simulation Sciences (joint venture of RWTH Aachen University and Forschungszentrum Jülich, Germany), Jülich, Germany

    Paolo Carloni

  4. Computational Biomedicine, Institute for Advanced Simulation IAS-5, Forschungszentrum Jülich, Jülich, Germany

    Paolo Carloni

  5. Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany

    Paolo Carloni

Authors
  1. Alejandro Giorgetti
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  2. Paolo Carloni
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Correspondence to Paolo Carloni .

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Editors and Affiliations

  1. Chemistry Department, Eotvos Lorand University, Budapest, Hungary

    Gábor Náray-Szabó

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Giorgetti, A., Carloni, P. (2014). Molecular Mechanics/Coarse-Grained Models. In: Náray-Szabó, G. (eds) Protein Modelling. Springer, Cham. https://doi.org/10.1007/978-3-319-09976-7_7

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