This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
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The structure, efficacy and mode of action of currently known mitochondrial uncoupler compounds vary widely. However, preliminary work at Newcastle has identified the UV-vis spectrum as a potential indicator of uncoupling activity. We propose to test this idea by calculating the UV-vis spectra of a library of known chemical compounds.
The primary language of the software to be used is Python. Density Functional Theory calculations of UV-vis spectra will be carried out with PySCF (https://github.com/pyscf/pyscf; https://github.com/Manohara-Ai/UV-Vis_and_Excitation_Energy), which depends on SciPy and NumPy,; other cheminformatics functions such as format conversions and the calculation of other molecular and structural properties will be carried out with RDKit. Pandas, geometric and matplotlib will also be needed. PySCF will run on non-gpu nodes, although it supports GPU acceleration.