PINE-SPARKY.2

PINE-SPARKY.2 integrates automated NMR chemical shift assignment, secondary-structure detection, flexibility and hydrophobic core prediction, and three-dimensional model calculation to support NMR-based structural biology of biological macromolecules.

Key Features:

• Chemical Shift Assignment and Verification: Automated assignment and verification of NMR chemical shifts to identify atomic environments within macromolecules.
• Automated Detection of Secondary Structural Elements: Automated detection of alpha-helices and beta-sheets from NMR data.
• Predictions of Flexibility and Hydrophobic Cores: Algorithms to predict regions of flexibility and to identify hydrophobic cores relevant to protein stability and function.
• Calculation of Three-Dimensional Structural Models: Calculation and refinement of three-dimensional structural models from NMR data to determine spatial atomic arrangements.

Scientific Applications:

• Atomic-level Structure Determination: Determination of atomic-level structures of proteins and other biological macromolecules using NMR data.
• Conformational Dynamics in Solution: Investigation of conformational changes and internal dynamics of macromolecules in solution.
• Protein–Ligand Interaction Characterization: Characterization of protein–ligand interactions detectable by NMR.

Methodology:

Performs automated chemical shift assignment and verification, automated secondary-structure detection, flexibility and hydrophobic core prediction algorithms, and calculation and refinement of three-dimensional structural models from NMR data.