BEAMS (BEAds Modelling System): a set of computer programs for the generation, the visualization and the computation of the hydrodynamic and conformational properties of bead models of proteins

No abstract is available for this paper.

• Publication year

  1997

• Venue

  European Biophysics Journal

• Publication date

  1997-05-13

• Fields of study

  Biology, Mathematics, Computer Science

• Identifiers
  DOI 10.1007/s002490050095
• 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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  1980influential reference
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