ISiCLE, or the in silico chemical library engine, is a software framework for high-accuracy chemical property calculation. ISiCLE takes an InChI or SMILES string as input, generates an initial 3D conformation, and subsequently optimizes this initial structure through molecular dynamics simulations and quantum chemistry optimizations. Finally, ISiCLE simulates desired properties (e.g. collision cross section, nuclear magnetic resonance chemical shifts) for each conformer yielded during molecular dynamics simulations to produce a single value, Boltzmann-weighted by relative Gibb's free energy, giving emphasis to properties from highly probable conformations.
If you would like to reference ISiCLE in an academic paper, we ask you include the following references:
- Colby, S.M., Thomas, D.G., Nuñez, J.R., Baxter, D.J., Glaesemann, K.R., Brown, J.M., Pirrung, M.A., Govind, N., Teeguarden, J.G., Metz, T.O. and Renslow, R.S., 2019. ISiCLE: A quantum chemistry pipeline for establishing in silico collision cross section libraries. Analytical Chemistry.
- Yesiltepe, Y., Nunez, J.R., Colby, S.M., Thomas, D.G., Borkum, M.I., Reardon, P.N., Washton, N.M., Metz, T.O., Teeguarden, J.T., Govind, N., and Renslow, R.S., 2018. An automated framework for NMR chemical shift calculations of small organic molecules. Journal of Cheminformatics.
- ISiCLE, version 2.0.0 http://github.com/pnnl/isicle (accessed MMM YYYY)
The first describes ISiCLE for CCS, the second describes ISiCLE for NMR chemical shifts, and the third is to cite the software package (update version and access date appropriately).
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