Biofuels & Protein Structure SFA

Protein Co-Evolutionary Analysis and Virtual Ligand Screening


A science focus area (SFA) is a research project funded by the Department of Energy (DOE) to further scientific advancement and support the DOE’s Office of Science mission. The ORNL SFA driven by Brian Davison at Oak Ridge National Laboratory (ORNL) aims to understand how to efficiently develop renewable biofuels from lignocellulosic biomass. To this end, it is important to study protein structure and binding of the byproducts generated throughout the process of biomass deconstruction. Better understanding the interactions between byproducts and enzymes helps to maximize biofuel production.

Collaborative Development Object

New Apps:

  • CCMPredPy Contact Mapping, will combine CCMPred, Blastp, and MUSCLE to allow researchers to go from a single sequence to a coevolutionary analysis and protein folding setup (KBase version: Beta App)
  • AutoDock Vina Protein-Ligand Docking, will apply the AutoDock VINA tool to a metabolite database. This will predict which specific byproducts affect which particular enzymes during biomass processing to optimally select for minimal inhibition. (KBase version: Beta App)
  • Import ModelProteinStructure from PDB File in Staging Area, allows users to import a PDB file from your staging area into your Narrative as a ProteinStructure data object (KBase version: Beta App)

New Narrative Tutorials:

  • In addition to bringing in new tools, the ORNL SFA will be creating new Narrative Tutorials to demonstrate how to use their new Apps

Additional Information

Meet the Members

SFA Manager for ORNL: Brian Davison1
SFA Technical Co-Managers: Barbara R. Evans1 and Paul A. Langan1 and Jeremy C. Smith1
SFA Contact: Julie Mitchell1 and Jeremy C. Smith1
KBase Contact: Chris Henry3,4
Lead Developer: Ada Sedova1
Participating Scientists: Hugh M. O’Neil1, Volker Urban1, Loukas Petridis1, Sai Venkatesh Pingali1, and Arthur Ragauskas1,2
Affiliations: 1Oak Ridge National Laboratory, 2University of Tennessee-Knoxville, 3Argonne National Laboratory, 4KBase