JAL

JAL analyzes hydration properties within structural ensembles of biomolecules to characterize solute–solvent interactions relevant to biomolecular stability and recognition.

Key Features:

• Atom-Centric Approach: Employs an atom-centric methodology to compute hydration properties for biomolecules including proteins and nucleic acids.
• Hydration Metrics and Utilities: Provides standard hydration metrics and specialized utilities to identify buried waters in molecular dynamics (MD) trajectories and to compute multiwater bridges around solutes.
• MD Trajectory Analysis: Operates on explicit-solvent molecular dynamics trajectories to interrogate solute–solvent interactions.

Scientific Applications:

• Tumor Suppressor Protein p53: Analyzes hydration characteristics of p53 to inform on water-mediated effects on its stability and function.
• Translation Initiation Factor eIF4E: Characterizes hydration dynamics around eIF4E relevant to its role in translation initiation.

Methodology:

Performs atom-centric computations on explicit-solvent molecular dynamics trajectories to compute hydration properties, identify buried waters, and detect multiwater bridges.