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Development of KBase-NWChem Interface for integration of molecular properties with Genome-Scale Metabolic Modeling


EMSL Project ID
50711

Abstract

One of the challenges to investigate natural and engineered biological systems at molecular-level is to accurately predict chemical properties of thousands of metabolites involved in cell metabolism. The overarching objective is to develop an interface between DOE’s KBase and DOE’s NWChem computational chemistry code to compute structural and thermodynamic properties of KBase compounds in an annotated genome-scale model. The NWChem predicted chemical properties such as the free energy of the formation of metabolites and reaction free energies will be subsequently used for accurate metabolic modeling to predict the metabolic fluxes and metabolites. KBase Narrative interface is built on the IPython platform and so the focus is to generate set of modules to automate the NWChem input, output, and linked the data type with KBase compounds. This would enable general KBase user to access advanced molecular modeling NWChem (EMSL) capabilities for their everyday research activities.

Project Details

Start Date
2019-01-21
End Date
2019-09-30
Status
Closed

Team

Principal Investigator

Marat Valiev
Institution
Environmental Molecular Sciences Laboratory

Team Members

Neeraj Kumar
Institution
Pacific Northwest National Laboratory