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 Henry^3,4
Lead Developer: Ada Sedova¹
Project Team: Hugh M. O’Neil¹, Volker Urban¹, Loukas Petridis¹, Sai Venkatesh Pingali¹, and Arthur Ragauskas^1,2
Affiliations: ¹Oak Ridge National Laboratory, ²University of Tennessee-Knoxville, ³Argonne National Laboratory, ⁴KBase

Resources

• ORNL SFA Biofuels – Visualization of Solvent Disruption of Biomass and Biomembrane
• Lead Developer GitHub
• GitHub Repository: Contact Mapping App
• GitHub Repository: AutoDock VINA App
• GitHub Repository: Import PDB File App