Benchmark of implicit solvent - force field combinations to study de Novo peptides

Author: Eric J. M. Lang - University of Bristol

Experimental description and characterization of the studied peptides can be found in: Baker, E., Bartlett, G., Crump, M. et al. Local and macroscopic electrostatic interactions in single α-helices. Nat Chem Biol 11, 221–228 (2015). https://doi.org/10.1038/nchembio.1739

A total of 5 peptides are studied here:

1. A₄(K₄E₄)A₄(K₄E₄)A₄ with an experimental helicity of 97%.
2. (K₄E₄)₂ and (E₄K₄)₂ with experimental helicity of 22% and 65%, resp.
3. (K₄E₄)₃ and (E₄K₄)₃ with experimental helicity of 62% and 74%, resp.

5 implicit solvent models (GB models) were tested:

• GBHCT, igb=1
• GBOBC, igb=2
• GBOBC2, igb=5
• GBn, igb=7
• GBn2, igb=8

13 force fields were tested: ff94,ff96,ff98,ff99, ff99SB, ff99SBildn, ff99SBnmr, ff03.r1, ff14SB, ff14SBonlysc, ff14ipq, fb15, ff15ipq

Simulations were performed with Amber16