Table 3 Protocol for nucleic acid‒target simulations.

From: Synthetic oligonucleotide antigens modified with locked nucleic acids detect disease specific antibodies

Process

Time interval (ns)

Structure minimization

2500 NAMD steps

DNA side chains, water molecules and ions released; rest fixed

0.1

DNA backbone except phosphorous atoms released but with some artificial bonds between complementary nucleobases; protein harmonic restrained

0.5

Harmonic constraints applied to DNA with some artificial bonds between complementary nucleobases

2

All atoms released

5

NVT ensemble, production simulation

100

  1. The simulations were carried out in the present study for each of the DNA and LNA/DNA sequences summarized in Table 1 and antibody ED-10.
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