About


Namdinator was developed by Rune Kidmose and Jesper Lykkegaard Karlsen.
Namdinators web service was created by Jonathan Juhl, Jonathan Søholm-Boesen (from Infobits) and Jesper Lykkegaard Karlsen.


Comments, suggestions and bug reports to: jelka@mbg.au.dk



Namdinator is described in this paper:

Namdinator - automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps.
Kidmose RT, Juhl J, Nissen P, Boesen T, Karlsen JL, Pedersen BP. IUCrJ 6, pp 526-531, (2019). [PubMed]


Namdinator is a pipeline tool and is dependent on the following software:
- AutoPSF, [link]
- VMD, Humphrey et al., J. Mol. Graph. 14 (1996), p33–38, 27–28.
- MDFF, Trabuco et al., Structure 16 (2008), p673–83.
- NAMD2, Phillips et al., J. Comput. Chem. 26 (2005), p1781–1802.
- phenix.real_space_refine, Adams et al., Acta Crystallogr. D Biol. Crystallogr. 66 (2010), p213–221.
- RosettaCommons, Alford et al., J. Chem. Theory Comput. 13 (2017), p3031–3048.