GeNMR

GeNMR generates three-dimensional protein structures from sequence data, NOE-based distance restraints, and NMR chemical shifts for NMR-based structure determination.

Key Features:

• Input Flexibility: Accepts sequence data, NOE-based distance restraints in XPLOR or CYANA formats, and chemical shift files from SHIFTY or BMRB.
• Rapid Processing: Produces an ensemble of PDB coordinates within 15-25 minutes depending on the complexity and completeness of the input restraints.
• Integrated Computational Pipeline: Combines genetic algorithms, homology modeling, chemical shift threading and prediction of torsion angles and distances from NOEs and shifts, ROSETTA-based structure generation, and simulated annealing with XPLOR-NIH for model optimization.

Scientific Applications:

• NMR-based protein structure determination: Derives three-dimensional protein structures from sequence data, NOE distance restraints, and NMR chemical shifts.
• Model refinement and validation: Generates ensembles of PDB coordinates for analyzing protein dynamics, function, and interactions and was validated on 90 proteins from the BioMagResBank.

Methodology:

Uses genetic algorithms for structure optimization; homology modeling; chemical shift threading and prediction of torsion angles and distances from NOEs and shifts; ROSETTA-based structure generation; and simulated annealing with XPLOR-NIH.