iMODFIT intro

iMODFIT is an efficient tool for flexible fitting of atomic structures into EM maps based on Normal Mode Analysis in Internal Coordinates. New 2016 version available! (v1.44)

Flexible fitting in internal coordinates with a reduced number of normal modes provides a natural way to alleviate overfitting distortions, such as poor resolution, map defects (e.g., scale inaccuracies, missing densities, resolution anisotropy), or even partial correspondence between the map and the atomic structure.

iMODFIT has been used by different groups to obtain impressive flexible fittings of:

ClpB disaggregase (Deville et al., Science Advances 2017)
Yeast R2TP complex (Rivera-Calzada et al., Structure 2017)
Human parechovirus 3 (Shakeel et al., Nat. Commun. 2016)
TcdA1 toxin (Gatsogiannis et al., Nat. Struct. Mol. Biol 2016)
Yeast RNA polymerase I (Pilsl et al., Nat. Commun. 2016)
Human cytoplasmic actomyosin complex (Von der Ecken et al., Nature 2016)
Human TFIID (Lauder et al., Nature 2016)
RavA ATPase (Kandiah et al., Sci Rep. 2016)
DnaKNBD-GrpE complex (Melero et al., JBC. 2015)
Human parechovirus 1 (Shakeel et al., J. Virol. 2015)
Mature HIV-1 capsid (Zhao et al., Nature. 2013, see Supplementary)
Coxsackievirus (Shakeel et al., J. Virol. 2013)
ATP synthase (Lau and Rubinstein, Nature 2012)
Yeast vacuolar ATPase (Oot et al., Structure 2012)


iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates (2013). López-Blanco J.R. and Chacón P. JSB 184(2):261–270