Protein Dynamics Simulations Using Coarse-Grained Models

No abstract is available for this paper.

• Publication year

  2018

• Venue

  Springer Series on Bio- and Neurosystems

• Publication date

  2018-11-29

• Fields of study

  Biology, Chemistry, Physics, Computer Science

• Identifiers
  DOI 10.1007/978-3-319-95843-9_3
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

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• Coarse-Grained Protein Models and Their Applications.

  2016influential reference
• Molecular dynamics simulations of large macromolecular complexes.

  2015cited by this paper
• Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment.

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  2014influential reference
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• Coarse-graining of multiprotein assemblies.

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• Coarse-grained molecular simulations of large biomolecules.

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• Molecular jamming--the cystine slipknot mechanical clamp in all-atom simulations.

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• Biomolecules under mechanical force

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• BSDB: the biomolecule stretching database

  2010cited by this paper
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