Table 1.
DNA Systems Used for Parameter Training and Validation a
| DNA sequence | Comment/Refrence |
|---|---|
| (1) d(CGCGAATTCGCG) | EcoR1 dodecamer, MD for 150 ns with Drude and C36 FFs, X-ray/NMR77–83 |
| (2) d(GCATTCTGAGTCAG) | JunFos, experimental BII content 69,72,84 |
| (3) d(ACACTACAATGTTGCAAT) | 3BSE, B form, X-ray 1.60 Å; disordered region 85 |
| (4) d(GAAGAGAAGC) | 1AXP, NMR, high purine content strand 87 |
| (5) d(CCGTCGACGG) | 1ZF7, B form, X-ray (1.5 Å) 86 |
| (6) d(CCGGGCCCGG) | 1ZF1, A form, X-ray (1.35 Å) 86 |
| (7) d(CGCATGCTACGC) | 2L8Q, B form, NMR 88 |
a
Of these, EcoR1 and 1ZF1 were used as training systems. Other sequences were utilized for the force field validation. All simulations were performed for 100 ns unless noted. Comment/Reference includes the PDB or NDB identifiers.