Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model.

In the one and two beads Coarse Grained (CG) models for proteins, the two conformational dihedrals ϕ and ψ that describe the backbone geometry are no longer present as explicit internal coordinates, thus the information contained in the Ramachandran plot cannot be used directly. We derive an analytical mapping between these dihedrals and the internal variable describing the backbone conformation in the one(two) beads CG models, namely the pseudo-bond angle and pseudo-dihedral between subsequent Cαs. This is used to derive a new density plot that contains the same information as the Ramachandran plot and can be used with the one(two) beads CG models. The use of this mapping is then illustrated with a new one bead polypeptide model that accounts for transitions between α-helices and β-sheets.

• Publication year

  2006

• Venue

  Journal of Chemical Theory and Computation

• Publication date

  2006-04-18

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1021/CT050294KPMID 19461947PMCID PMC2600716
• 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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