REDCRAFT

REDCRAFT determines protein structures from Residual Dipolar Couplings (RDCs) measured by Nuclear Magnetic Resonance (NMR) spectroscopy to enable structural modeling when NOE-derived distance restraints are limited, such as in perdeuterated proteins.

Key Features:

• RDC-based structure determination: Performs protein structure modeling using Residual Dipolar Coupling (RDC) data as the primary experimental restraint.
• Adaptive Decimation (AD): Implements Adaptive Decimation to improve robustness against missing or noisy RDC data.
• Perdeuterated protein applicability: Suited for cases with sparse NOE data, including perdeuterated proteins.
• Experimental and simulated RDC support: Handles experimentally collected RDCs for proteins of 50–145 residues and simulated RDCs for proteins of 145–573 residues.
• Validation against NOE structures: Enables comparison to NOE-based structures, demonstrating performance such as a BB-RMSD of 1.0 Å for PF.2048.1.
• Integration with other NMR parameters: Can be combined with chemical shifts and NOEs as an optional strategy to enhance structure determination.

Scientific Applications:

• Small-to-medium protein structure determination: Determining structures of proteins in the 50–145 residue range using experimental RDCs.
• Large protein modeling with simulated data: Modeling larger proteins (145–573 residues) using simulated RDC datasets.
• Perdeuterated protein analysis: Structural characterization of perdeuterated proteins where NOE data are limited.
• Method validation and comparison: Validating RDC-derived models against high-quality NOE-based structures, exemplified by PF.2048.1.

Methodology:

Computationally uses Residual Dipolar Coupling (RDC) data (experimental or simulated) with Adaptive Decimation (AD) for structure modeling and assesses agreement to reference NOE-based structures via backbone RMSD (BB-RMSD).