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. 2016 May 13;12(5):e1004935. doi: 10.1371/journal.pcbi.1004935

Table 1. Summary of MD simulations.

Simulated Structure Simulation Name Duration #atoms
GAL11-ABD1/GCN4-cAD GAL11-ABD1/GCN4-cAD _aMD_no1 1 μs 45,489
(PDB#2LPB-model 1) GAL11-ABD1/GCN4-cAD _aMD_no2 1 μs 45,489
GAL11-ABD1/GCN4-cAD _aMD_no3 1 μs 45,489
GAL11-ABD1/GCN4-cAD _aMD_no4 1 μs 45,489
GCN4-cAD GCN4_aMD_no1 1 μs 32,551
(de novo starting structure) GCN4_aMD_no2 1 μs 32,551
GCN4_aMD_no3 1 μs 32,551
GCN4_aMD_no4 1 μs 32,551
GAL11-ABD1 GAL11-ABD1 _aMD_no1 1 μs 42,355
(PDB#2LPB; without GCN4) GAL11-ABD1 _aMD_no2 1 μs 42,355
GAL11-ABD1 _aMD_no3 1 μs 42,355
GAL11-ABD1 _aMD_no4 1 μs 42,355
cAD-like07 cAD-like07_aMD_no1 1 μs 28,131
(de novo starting structure)
cAD-like96 cAD-like96_aMD_no1 1 μs 28,424
(de novo starting structure)
GAL11-ABD1/GCN4-cADlike96 GAL11-ABD1/cAD-like96_aMD_no1 1 μs 46,862
(PDB#2LPB; in silico GAL11-ABD1/cAD-like96_aMD_no2 1 μs 46,862
mutagenized GCN4) GAL11-ABD1/cAD-like96_aMD_no3 1 μs 46,862
GAL11-ABD1/cAD-like96_aMD_no4 1 μs 46,862