Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations

No abstract is available for this paper.

• Publication year

  2014

• Venue

  Proceedings of the National Academy of Sciences of the United States of America

• Publication date

  2014-10-13

• Fields of study

  Medicine, Chemistry

• Identifiers
  DOI 10.1073/pnas.1407768111PMID 25313044PMCID PMC4217416
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2012influential reference
• Context and force field dependence of the loss of protein backbone entropy upon folding using realistic denatured and native state ensembles.

  2012influential reference
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  2009influential reference
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  2009cited by this paper
• Protein side-chain dynamics and residual conformational entropy.

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• Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins.

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• Scalable molecular dynamics with NAMD

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• The magnitude of the backbone conformational entropy change in protein folding

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• Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation

  1994cited by this paper
• Alpha-helix-forming propensities in peptides and proteins.

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