Abstract
Proteins that bind small molecules (ligands) can be used as biosensors, signal modulators, and sequestering agents. When naturally occurring proteins for a particular target ligand are not available, artificial proteins can be computationally designed. We present a protocol based on RosettaLigand to redesign an existing protein pocket to bind a target ligand. Starting with a protein structure and the structure of the ligand, Rosetta can optimize both the placement of the ligand in the pocket and the identity and conformation of the surrounding sidechains, yielding proteins that bind the target compound.
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Acknowledgements
This work was supported through NIH (R01 GM099842, R01 DK097376, R01 GM073151) and NSF (CHE 1305874). RM is further partially supported by grant from the RosettaCommons.
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Moretti, R., Bender, B.J., Allison, B., Meiler, J. (2016). Rosetta and the Design of Ligand Binding Sites. In: Stoddard, B. (eds) Computational Design of Ligand Binding Proteins. Methods in Molecular Biology, vol 1414. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3569-7_4
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DOI: https://doi.org/10.1007/978-1-4939-3569-7_4
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