When using 3D-DART please cite the following article:
M. van Dijk and A.M.J.J. Bonvin (2009) "3D-DART: a DNA structure modelling server"
Nucl. Acids Res., 37 (Web Server Issue):W235-W239 (doi:10.1093/nar/gkp287)
For an explanation of the various options and access to sample data please consult the help pages accessible by clicking on the help link available at the bottom right corner of every dialog
Step 1. Build Nucleic Acid structure from scratch or base-pair(step) parameter file
Give your structure a name
Provide the nucleic acid sequence (5'->3')
Number of repeats
Build from user defined parameter file
Build from PDB structure file
Nucleic acid type
 
Generate Calladine-Drew plots (For visualization purposes. In ALCHEMY format)
One block per base-pair/base
Two blocks per base-pair

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Step 2. Nucleic Acids Modeling options
Modelling mode Global Local
 
Define nucleic acid bending
Define bend angle range (global:1-5 or 3,local:3,4,2,3,..)
Define bend-angle step size
Define bend angle orientation range (global:1-5 or 3,local:3,4,2,3,..)
Define bend angle orientation step size
Define bend zone
Base-pair used as origin in global reference frame. (Optional, default is sequence center)
Helical phasing (base-pairs/turn) (Optional, default is 10 bp/turn)
 
Define custom values for base-pair step parameters.
Shift
Slide
Rise
Tilt
Roll
Twist
 
Define custom values for base-pair parameters.
Shear
Stretch
Stagger
Buckle
Propeller-Twist
Opening

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Step 3. PDB formatting options
Convert IUPAC to CNS notation
Convert nucleic acid 1 letter to 3 letter notation
Set PDB chain id
Renumber residues starting from

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Step 4. For HADDOCK users
Make PDB HADDOCK ready
DNA/RNA restraints file
Setup the DNA/RNA restraint file for use in HADDOCK
 
Planarity restraints
Use Watson-Crick base-pair planarity
Use base planarity
 
Watson-Crick base-pair restraints
Pick Watson-Crick H-bond restraint values from structure
Lower H-bond error range limit
Upper H-bond error range limit
Set sugar-pucker dihedral angle restraints
Pick the dihedral angles of the sugar pucker from the input structure (automatic restraint definition)
 
In case of manual restraint definition define the conformational groups below
Conformation of group 1
Conformation of group 1
Start residue
End residue
User defined pucker restraints for group 1 (angle average and error range)
dihedral C1'-C2'-C3'-C4'
dihedral C5'-C4'-C3'-C2'
dihedral C1'-O4'-C4'-C5'
Conformation of group 2
Conformation of group 2
Start residue
End residue
User defined pucker restraints for group 2 (angle average and error range)
dihedral C1'-C2'-C3'-C4'
dihedral C5'-C4'-C3'-C2'
dihedral C1'-O4'-C4'-C5'
Conformation of group 3
Conformation of group 3
Start residue
End residue
User defined pucker restraints for group 3 (angle average and error range)
dihedral C1'-C2'-C3'-C4'
dihedral C5'-C4'-C3'-C2'
dihedral C1'-O4'-C4'-C5'
Set phosphate backbone dihedral angle restraints
Pick the dihedral angles of the phosphate backbone from the input structure (automatic restraint definition)
 
In case of manual restraint definition define the conformational groups below
Conformation of group 1
Conformation of group 1
Start residue
End residue
User defined phosphate backbone restraints for group 1 (angle average and error range)
alpha dihedral O3'-P-O5'-C5'
beta dihedral P-O5'-C5'-C4'
gamma dihedral O5'-C5'-C4'-C3'
delta dihedral C5'-C4'-C3'-O3'
epsilon dihedral C4'-C3'-O3'-P
zeta dihedral C3'-O3'-P-O5'
Conformation of group 2
Conformation of group 2
Start residue
End residue
User defined phosphate backbone restraints for group 2 (angle average and error range)
alpha dihedral O3'-P-O5'-C5'
beta dihedral P-O5'-C5'-C4'
gamma dihedral O5'-C5'-C4'-C3'
delta dihedral C5'-C4'-C3'-O3'
epsilon dihedral C4'-C3'-O3'-P
zeta dihedral C3'-O3'-P-O5'
Conformation of group 3
Conformation of group 3
Start residue
End residue
User defined phosphate backbone restraints for group 3 (angle average and error range)
alpha dihedral O3'-P-O5'-C5'
beta dihedral P-O5'-C5'-C4'
gamma dihedral O5'-C5'-C4'-C3'
delta dihedral C5'-C4'-C3'-O3'
epsilon dihedral C4'-C3'-O3'-P
zeta dihedral C3'-O3'-P-O5'

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