Dynameomics Resources
Dynameomics is an initiative started in the Daggett Lab at the University of Washington (USA) to characterise the dynamics and unfolding of all known structures in protein fold space. Many propensities libraries and rotamer libraries created as part of the Dynameomics initiative can be found through this following link. These can be used in understanding protein and peptides structure, as well as design tools to drive and optimise protein engineering and peptide drug design.
Structural Library of Intrinsic Residue Propensities (SLIRP)
References for the resources that Clare Towse contributed to are:
Dynameomics Entropy Dictionary (DED)
-
Towse CL, Akke M, Daggett V. The Dynameomics Entropy Dictionary: A Large-Scale Assessment of Conformational Entropy across Protein Fold Space. J Phys Chem B. 2017 Apr 19. doi: 10.1021/acs.jpcb.7b00577. PubMed PMID: 28375008.
Backbone Conformational Propensities (AAXAA, GGXGG, and heterochiral systems)
-
Childers MC, Towse CL, Daggett V. The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design. Protein Eng Des Sel. 2016 Jul;29(7):271-80. doi: 10.1093/protein/gzw023. PubMed PMID: 27284086; PubMed Central PMCID: PMC4917059.
-
Towse CL, Vymetal J, Vondrasek J, Daggett V. Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series. Biophys J. 2016 Jan 19;110(2):348-61. doi: 10.1016/j.bpj.2015.12.008. PubMed PMID: 26789758.
-
Towse CL, Hopping G, Vulovic I, Daggett V. Nature versus design: the conformational propensities of D-amino acids and the importance of side chain chirality. Protein Eng Des Sel. 2014 Nov;27(11):447-55. doi: 10.1093/protein/gzu037. PubMed PMID: 25233851.
Rotamer Libraries
- Towse CL, Rysavy SJ, Vulovic IM, Daggett V. New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities. Structure. 2016 Jan 5;24(1):187-99. doi: 10.1016/j.str.2015.10.017. PubMed PMID: 26745530.
Peyton Lab 