qFit 3

qFit 3 generates multiconformer models from X-ray crystallography and cryo-electron microscopy (cryo-EM) electron density maps to represent protein conformational ensembles and ligand variability.

Key Features:

• Multiconformer modeling: Generates multiconformer models that capture multiple protein and ligand conformations consistent with X-ray and cryo-EM electron density maps.
• Automated alternate-conformation identification: Identifies and models internally consistent sets of alternate conformations across residues and small-molecule ligands.
• Exhaustive conformer combination evaluation: Evaluates an extensive array of combinations of sidechain conformers, backbone fragments, and small-molecule ligands to explain observed electron density.
• Parsimonious model selection: Selects parsimonious multiconformer models that balance fit to electron density with internal consistency across conformational states.

Scientific Applications:

• Protein dynamics characterization: Enables characterization of protein conformational ensembles and backbone and sidechain heterogeneity from crystallography and cryo-EM data.
• Structure-based drug discovery: Informs analysis of ligand binding sites and conformational flexibility relevant to drug design and ligand optimization.

Methodology:

Evaluates an extensive array of conformer combinations and identifies an internally consistent set of alternate conformations that together best explain X-ray or cryo-EM electron density maps to produce parsimonious multiconformer models.