Fragment Scope

Available Data Types

Software

Cartesian analysis

• RMSd, RMSf, Radius of Giration, SASA

Base

Average values, Plot (Sequence), Plot (Time)

pTraj (14),
Gromacs (15)

Backbone geometry

• BI/BII population
• Sugar puckering (N,E,S,W population)
• Proportion of alpha/gamma torsions
• Torsions (a, b, g, e, z, c, phase)

Base

Average values, Plot (Sequence), Plot (Time)

Curves+ (13)

Translation Base Pair Axis

• X-Displacement, Y-Displacement

Base Pair

Plot (Sequence), Plot (Time)

Curves+ (13)

Rotational Base Pair Axis

• Inclination, Tip

Base Pair

Plot (Sequence), Plot (Time)

Curves+ (13)

Translation Base Pair Helical parameters

• Shear, Stretch, Stagger

Base Pair

Plot (Sequence), Plot (Time)

Curves+ (13)

Rotation Base Pair Helical parameters

• Buckle, Opening, Propeller

Base Pair

Plot (Sequence), Plot (Time)

Curves+ (13)

Translation Base Pair Step parameters

• Rise, Slide, Shift

BP Step

Plot (Sequence), Plot (Time)

Curves+ (13)

Rotational Base Pair Step parameters

• Roll, Tilt, Twist

BP Step

Plot (Sequence), Plot (Time)

Curves+ (13)

Groove dimensions

• Major and Minor grooves (depth, width)

BP Step

Plot (Sequence), Plot (Time)

Curves+ (13)

Interactions

• Base Pair Canonical Hydrogen Bonds (distances)
• Hydrogend Bond energies
• Stacking Energies

Base,
BP Step

Plot (sequence), Plot (Time),
Contact Maps

Stiffness analysis

• Stiffness force constants (Twist, roll, Tilt, Rise, Shift, Slide)
• Complete stiffness Matrix

Base Pair Step

Curves+ (13)

NMR Observables

• Vicinal J-Couplings
• Nuclear Overhauser Effect (NOE)

Base

Values, Plot (Time)
2D NOE Plots

Principal component analysis

• EigenValues & EigenVectors
• Collectivity index
• EigenVector Stiffness constant
• Animated Trajectories
• Trajectory projections
  

Collective

Values.
Animated Traj 3D view (JsMol)
Projections Time Plots

PCASuite (16,17)

Trajectory video

Collective

Standard video formats,
3D view

VMD (18)