--All-Atom Model-- 
Whitford PC, et al. (2009) Proteins: Structure, Function, Bioinformatics, 75, 430-441. 

--Contact Potentials--
Shadow Algorithm: Noel JK, Whitford PC, Onuchic, JN (2012) J Phys Chem, 116, 8692-8702.

--SMOG with AMBER bonded terms--
SBM_AA-amber-bonds force field is defined in:
Whitford PC, Jiang W, Serwer P (2020) Viruses, 12, 1273.

--Modified residues--
Singh, Itoh, Del'Olio, Hassan, Naschberger, Flygaard, Nobe, Izumikawa, Aibara, Andrell, Whitford, Barrientos, Taoka, and Amunts.
Nature Communications, 15, 4272, 2024. DOI: 10.1038/s41467-024-48163-x

--SAH and NAD--
Zgadzay, Mirabello, Wanes, Panek, Chauhan, Nystedt, Zikova, Whitford, Gahura, and Amunts.
Structure, 2025. DOI: 10.1016/j.str.2025.08.002
