Biofuels & Protein Structure SFA

Protein Co-Evolutionary Analysis and Virtual Ligand Screening

The Biofuels and Protein Structure Science Focus Area (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 Projects

Functionality and Tools

  • CCMPredPy Contact Mapping: Combine CCMPred, Blastp, and MUSCLE to allow researchers to go from a single sequence to a coevolutionary analysis and protein folding setup. (Beta-only)
  • AutoDock Vina Protein-Ligand Docking: 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. (Beta-only)
  • 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. (Beta-only)

    Additional Information

    Meet the Members

    SFA Manager: Brian Davison1
    SFA Technical Co-Manager: Barbara R. Evans1
    SFA Principal Investigators: Julie Mitchell1 and Jeremy C. Smith1
    KBase Contact: Chris Henry3,4
    Lead Developer: Ada Sedova1
    Project Team: 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