ProteinDNANonSpecificInteraction #

ProteinDNANonSpecificInteraction is a coarse-grained model of hydrogen bond, especially formed between protein and DNA.

It is developed in the following paper.

• T.Niina‡, G.B.Brandani‡, C.Tan and S.Takada, (2017) PLoS Comput Biol. (‡: co-1st)

Example #

[[forcefields.global]]
interaction = "PDNS"
potential   = "PDNS"
spatial_partition.type   = "VerletList"
spatial_partition.margin = 0.5
sigma = 1.0
delta = 0.17453
parameters  = [
{index =    2, kind = "DNA", S3 = 1},
{index =    5, kind = "DNA", S3 = 4},
# ...
{index = 1000, offset = 100, kind = "Protein", PN =  999, PC = 1001, k = -1.2, r0 = 5.0, theta0 = 1.57, phi0 = 1.73},
{index = 1023, offset = 100, kind = "Protein", PN = 1022, PC = 1024, k = -1.2, r0 = 6.0, theta0 = 1.57, phi0 = 1.73},
# ...
]

Input Reference #

• interaction: String
  • Name of the interaction. Here, it is "PDNS".
• potential: String
  • Name of the potential. Here, it is "PDNS".
• sigma: Floating
  • The width of the attractive potential along the radial direction.
• delta: Floating
  • The width of the attractive potential along the angle direction.
• parameters: Array of Tables
  • index: Integer
    • The index of the particle.
    • In DNA case, the index of the phosphate.
  • offset: Integer (Optional. By default, 0)
    • Offset of the index.
  • kind: String
    • There are 2 kinds of particles, DNA and Protein.
  • S3: Integer
    • Only required for DNA. The index of sugar particle of adjacent nucleotide towords the 3’ end.
  • PN, PC: Integer
    • Only required for Protein. The adjacent particle towords N- and C-terminus, respectively.
  • k: Floating
    • The strength of the potential.
  • r0, theta0, phi0: Floating
    • The native conformation.