Benchmark sets
1. Wang, C., Bradley, P. & Baker, D. Protein-protein docking with backbone flexibility. J Mol Biol 373, 503–19 (2007).
2. Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP. Toward better refinement of comparative models: predicting loops in inexact environments. Proteins. 2008 Aug 15;72(3):959-71. doi: 10.1002/prot.21990. PMID: 18300241; PMCID: PMC2764870.

CCD / benchmark sets
3. Canutescu, A. A. & Dunbrack, R. L. Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci. 12, 963–72 (2003).
4. Wang, C., Bradley, P. & Baker, D. Protein-protein docking with backbone flexibility. J Mol Biol 373, 503–19 (2007).

KIC
5. Mandell, DJ, Coutsias, EA, Kortemme, T. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. 2009.
Nat Methods 6(8):551-2. doi: 10.1038/nmeth0809-551.

KIC with fragments
6. Fernandez, A. J., Daniel, E. J. P., Mahajan, S. P., Gray, J. J., Gerken, T. A., Tabak, L. A. & Samara, N. L. The structure of the colorectal cancer-associated enzyme GalNAc-T12 reveals how nonconserved residues dictate its function. Proc. Natl. Acad. Sci. U. S. A. 116, 20404–20410 (2019).

NGK
7. Kapp, G. T., Liu, S., Stein, A., Wong, D. T., Remenyi, A., Yeh, B. J., Fraser, J. S., Taunton, J., Lim, W. A. & Kortemme, T. Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc. Natl. Acad. Sci. 109, 5277–5282 (2012).
8. Stein, A. & Kortemme, T. Improvements to robotics-inspired conformational sampling in rosetta. PLoS One 8, e63090 (2013).
