Microsecond time-scale molecular dynamics simulations of the ABC oligomers

The collaborative effort of the ABC laboratories allowed the collection of microsecond scale molecular dynamics simulations on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences, using the Amber forcefield (parm99bsc0). The full MD dataset contains more than 35 million conformational snapshots of B-DNA in physiological salt conditions.

Observations include highly sequence-dependent occupancies of backbone BI/BII states, that are related to the sequence dependent multimodality of the three helical parameters shift, slide and twist.