Protein-Ligand MD Simulation & Binding Free Energy Calculation

Output

Backbone Root Mean Square Deviation to assess overall structural stability.

Evaluates the positional stability of the ligand within the binding pocket.

Highly accurate MM/PBSA calculated binding affinities and energy decomposition.

Root Mean Square Fluctuation detailing per-residue flexibility.

Advanced fluctuation analysis isolating essential collective motions.

Measures the compactness and folding stability of the protein complex.

SASA analysis to monitor surface exposure and hydrophobic core integrity.

Tracks the number of intermolecular hydrogen bonds formed over time.

Schematic representation of persistent protein-ligand contacts.

Protein-Ligand Interaction Profiler identifying Pi-stacking and salt bridges.

Time-evolution of alpha-helices and beta-sheets throughout the trajectory.

PCA identifying the dominant modes of structural variation.

3D contour mapping to identify metastable conformational states.

DCCM matrix revealing correlated and anti-correlated residue motions.

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Tool Name	Purpose	Citation