title: Protein backbone ensemble generation explores the local structural space of unseen natural homologs.
abstract: Mutations in homologous proteins affect changes in the backbone conformation that involve a complex interplay of forces which are difficult to predict. Protein design algorithms need to anticipate these backbone changes in order to accurately calculate the energy of the structure given an amino acid sequence, without knowledge of the final, designed sequence. This is related to the problem of predicting small changes in the backbone between highly similar sequences.
  
  
  
  We explored the ability of the Rosetta suite of protein design tools to move the backbone from its position in one structure (template) to its position in a close homologous structure (target) as a function of the diversity of a backbone ensemble constructed using the template structure, the percent sequence identity between the template and target, and the size of local zone being considered in the ensemble. We describe a pareto front in the likelihood of moving the backbone toward the target as a function of ensemble diversity and zone size. The equations and protocols presented here will be useful for protein design.
  
  
  
  PyRosetta scripts available at www.bioinfo.rpi.edu/bystrc/downloads.html#ensemble
  
  
  
  bystrc@rpi.edu.
authors.affiliation: Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA.
authors.forename: Christian D
authors.initials: CD
authors.lastname: Schenkelberg
authors.affiliation: Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Bystroff
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins