PALES

PALES predicts sterically induced alignment tensors and residual dipolar couplings from three-dimensional structures of proteins, nucleic acids, oligosaccharides, and small molecules to support interpretation of liquid-state NMR experiments.

Key Features:

• Prediction of Alignment Tensors: Estimates both the magnitude and orientation of sterically induced alignment tensors and resultant residual dipolar couplings from molecular structures.
• Applicability to Various Molecules: Supports proteins, nucleic acids, oligosaccharides, and small molecules as input solutes.
• Consideration of Molecular Shape and Charge Distribution: Incorporates three-dimensional molecular shape and 3D charge distribution into alignment predictions.
• Support for Multiple Orienting Media: Adapts predictions to neutral and charged orienting media to reflect different experimental environments.

Scientific Applications:

• Liquid-state NMR interpretation: Provides predicted residual dipolar couplings and alignment tensors to aid analysis of NMR experiments.
• Structural biology and conformational analysis: Enables assessment of conformational states and orientation of biomolecules based on predicted alignment.
• Study of molecular interactions: Facilitates investigation of biomolecular interactions by providing alignment information that constrains relative orientations.

Methodology:

Uses a known three-dimensional coordinate file of the solute and simulates how molecular shape and three-dimensional charge distribution influence alignment within neutral or charged media to predict alignment tensors and residual dipolar couplings.