Paper Citing NAMD - Abstract
Tuukkanen, Anne; Huang, Bingding; Henschel, Andreas; Stewart, Francis; Schroeder, Michael
Structural modeling of histone methyltransferase complex Set1C from Saccharomyces cerevisiae using constraint-based docking
PROTEOMICS, 10:4186-4195, DEC 2010
Set1C is a histone methyltransferase playing an important role in yeast gene regulation Modeling the structure of this eight subunit protein complex is an important open problem to further elucidate its functional mechanism Recently, there has been progress in modeling of larger complexes using constraints to restrict the combinatorial explosion in binary docking of subunits Here we model the subunits of Set1C and develop a constraint based docking approach which uses high quality protein interaction as well as functional data to guide and constrain the combinatonal assembly procedure We obtained 22 final models The core complex consisting of the subunits Set1 Bre2 Sdc1 and Swd2 is conformationally conserved in over half of the models thus giving high confidence We characterize these high confidence and the lower confidence interfaces and discuss implications for the function of Set1C
